bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of the frequency of putative prostate cancer stem cells in primary and metastatic prostate cancer
Authors: Eaton Colby L. , Colombel Marc , van der Pluijm Gabri , Cecchini Marco , Wetterwald Antoinette , Lippitt Jenny , Rehman Ishtiaq , Hamdy Freddie , Thalman George 
Published: February 2010

AbstractBACKGROUNDTumour cells with a stem cell‐like phenotype have recently been identified in prostate tumors and it has been suggested that this population may be responsible for the diversity of cell types within tumors and also for the initiation of metastases. These cells carry a number of defined markers: they are cd133 and cd44+ve and express high levels of α2β1 integrin. In this study we have, for the first time, assessed matched primary and bone marrow biopsies from prostate cancer patients for the distribution of cells carrying these and a number of other putative stem cell markers.METHODSEleven matched (primary and bone metastasis) specimens from prostate cancer patients were assessed for the presence of cd133, cd44, α2β1 integrin, CXCR4, c‐met, α6 integrin, and nestin using immunohistochemistry and stain intensity and distribution scored.RESULTSIn the bone metastases, tumor cells staining positively for cd133 were detected at low frequency in ∼50% of samples. Staining for nestin was confined to endothelium. Positive staining of tumor cells for the other antigens was present at variable frequency in >70% of metastases with the exception of CXCR4 which was absent from all but 2 specimens. Where positive staining of tumor cells was present in the metastasis, cells staining for each antigen were present in the matched primary with the exception of cd44 which was absent in all but 2/11 matched primary tissues.CONCLUSIONSIn established metastases no single or combination of marker expression profiles identify the established metastatic phenotype, although cd44 expression was shown to be more frequent in metastases that in primary cancers. Prostate 70: 875–882, 2010. © 2010 Wiley‐Liss, Inc.
Genetic alterations and changes in expression of histone demethylases in prostate cancer
Authors: Suikki Hanna E. , Kujala Paula M. , Tammela Teuvo L.J. , van Weerden Wytske M. , Vessella Robert L. , Visakorpi Tapio 
Published: February 2010

AbstractBACKGROUNDHistone demethylases LSD1, JHDM2A, and GASC1 have been suggested to function as androgen receptor co‐activators, and to be involved in prostate cancer (PC) progression. We aim to identify genetic alterations and changes in expression of these genes in PC.METHODSPC cell lines, xenografts as well as clinical specimens were screened for mutations using denaturating high‐performance liquid chromatography and sequencing, and for expression alterations by using quantitative RT‐PCR and immunohistochemistry.RESULTSOnly known single nucleotide polymorphisms, but no mutations, were found in these genes. JHDMA2 mRNA expression was slightly increased (P < 0.05) in PC compared with benign prostate hyperplasia (BPH), whereas the expression of GASC1 was slightly higher (P < 0.05) in castration‐resistant PC (CRPC) compared with untreated PC or BPH. The mRNA expression of LSD1 was not altered in PC. The expression of LSD1 protein was somewhat, although not statistically significantly (P = 0.0521) lower in CRPC compared with untreated PC. In prostatectomy specimens, the level of LSD1 protein expression was associated with low pT‐stage (P = 0.0402), but not with Gleason score or progression‐free survival.CONCLUSIONSAs no genetic alterations and only very modest expression changes were found, it is unlikely that LSD1, JHDM2A, or GASC1 play a major role in the progression of PC. Prostate 70: 889–898, 2010. © 2010 Wiley‐Liss, Inc.
Binding of calcium is sensed structurally and dynamically throughout the second calcium‐binding domain of the sodium/calcium exchanger
Authors: Breukels Vincent , Vuister Geerten W. 
Published: February 2010

AbstractWe report the effects of Ca2+ binding on the backbone relaxation rates and chemical shifts of the AD and BD splice variants of the second Ca2+‐binding domain (CBD2) of the sodium–calcium exchanger. Analysis of the Ca2+‐induced chemical shifts perturbations yields similar KD values of 16–24 μM for the two CBD2‐AD Ca2+‐binding sites, and significant effects are observed up to 20 Å away. To quantify the Ca2+‐induced chemical shift changes, we performed a comparative analysis of eight Ca2+‐binding proteins that revealed large differences between different protein folds. The CBD2 15N relaxation data show the CBD2‐AD Ca2+ coordinating loops to be more rigid in the Ca2+‐bound state as well as to affect the FG‐loop located at the opposite site of the domain. The equivalent loops of the CBD2‐BD splice variant do not bind Ca2+ and are much more dynamic relative to both the Ca2+‐bound and apo forms of CBD2‐AD. A more structured FG‐loop in CBD2‐BD is suggested by increased S2 order parameter values relative to both forms of CBD2‐AD. The chemical shift and relaxation data together indicate that, in spite of the small structural changes, the Ca2+‐binding event is felt throughout the molecule. The data suggest that the FG‐loop plays an important role in connecting the Ca2+‐binding event with the other cytosolic domains of the NCX, in line with in vivo and in vitro biochemical data as well as modeling results that connect the CBD2 FG‐loop with the first Ca2+‐binding domain of NCX. Proteins 2010. © 2010 Wiley‐Liss, Inc.
Contact prediction for beta and alpha‐beta proteins using integer linear optimization and its impact on the first principles 3D structure prediction method ASTRO‐FOLD
Authors: Rajgaria R. , Wei Y. , Floudas C. A. 
Published: February 2010

AbstractAn integer linear optimization model is presented to predict residue contacts in β, α + β, and α/β proteins. The total energy of a protein is expressed as sum of aCαCαdistance dependent contact energy contribution and a hydrophobic contribution. The model selects contact that assign lowest energy to the protein structure as satisfying a set of constraints that are included to enforce certain physically observed topological information. A new method based on hydrophobicity is proposed to find the β‐sheet alignments. These β‐sheet alignments are used as constraints for contacts between residues of β‐sheets. This model was tested on three independent protein test sets and CASP8 test proteins consisting of β, α + β, α/β proteins and it was found to perform very well. The average accuracy of the predictions (separated by at least six residues) was ∼61%. The average true positive and false positive distances were also calculated for each of the test sets and they are 7.58 Å and 15.88 Å, respectively. Residue contact prediction can be directly used to facilitate the protein tertiary structure prediction. This proposed residue contact prediction model is incorporated into the first principles protein tertiary structure prediction approach, ASTRO‐FOLD. The effectiveness of the contact prediction model was further demonstrated by the improvement in the quality of the protein structure ensemble generated using the predicted residue contacts for a test set of 10 proteins. Proteins 2010. © 2010 Wiley‐Liss, Inc.
Structural rationale for the short branched substrate specificity of the glycogen debranching enzyme GlgX
Authors: Song Hyung‐Nam , Jung Tae‐Yang , Park Jong‐Tae , Park Byung‐Chul , Myung Pyung Keun , Boos Winfried , Woo Eui‐Jeon , Park Kwan‐Hwa 
Published: February 2010

AbstractGlycogen serves as major energy storage in most living organisms. GlgX, with its gene in the glycogen degradation operon, functions in glycogen catabolism by selectively catalyzing the debranching of polysaccharide outer chains in bacterial glycosynthesis. GlgX hydrolyzes α‐1,6‐glycosidic linkages of phosphorylase‐limit dextrin containing only three or four glucose subunits produced by glycogen phosphorylase. To understand its mechanism and unique substrate specificity toward short branched α‐polyglucans, we determined the structure of GlgX from Escherichia Coli K12 at 2.25 Å resolution. The structure reveals a monomer consisting of three major domains with high structural similarity to the subunit of TreX, the oligomeric bifunctional glycogen debranching enzyme (GDE) from Sulfolobus. In the overlapping substrate binding groove, conserved residues Leu270, Asp271, and Pro208 block the cleft, yielding a shorter narrow GlgX cleft compared to that of TreX. Residues 207–213 form a unique helical conformation that is observed in both GlgX and TreX, possibly distinguishing GDEs from isoamylases and pullulanases. The structural feature observed at the substrate binding groove provides a molecular explanation for the unique substrate specificity of GlgX for G4 phosphorylase‐limit dextrin and the discriminative activity of TreX and GlgX toward substrates of varying lengths. Proteins 2010. © 2010 Wiley‐Liss, Inc.
Dewetting transitions in protein cavities
Authors: Young Tom , Hua Lan , Huang Xuhui , Abel Robert , Friesner Richard , Berne B. J. 
Published: February 2010

AbstractIn a previous analysis of the solvation of protein active sites, a drying transition was observed in the narrow hydrophobic binding cavity of Cox‐2. With the use of a crude metric that often seems able to discriminate those protein cavities that dry from those that do not, we made an extensive search of the PDB, and identified five other proteins that, in molecular dynamics simulations, undergo drying transitions in their active sites. Because such cavities need not desolvate before binding hydrophobic ligands they often exhibit very large binding affinities. This article gives evidence that drying in protein cavities is not unique to Cox‐2. Proteins 2010. © 2010 Wiley‐Liss, Inc.
Novel use of nanostructured alumina as an insecticide
Authors: Stadler Teodoro , Buteler Micaela , Weaver David K 
Published: February 2010

AbstractBACKGROUND: The worldwide need to produce an inexpensive and abundant food supply for a growing population is a great challenge that is further complicated by concerns about risks to environmental stability and human health triggered by the use of pesticides. The result is the ongoing development of alternative pest control strategies, and new, lower‐risk insecticidal molecules. Among the recent technological advances in agricultural science, nanotechnology shows considerable promise, although its development for use in crop protection is in its initial stages.RESULTS: This study reports for the first time the insecticidal effect of nanostructured alumina. Two species were used as model organisms, Sitophilus oryzae L. and Rhyzopertha dominica (F.), which are major insect pests in stored food supplies throughout the world. Both species experienced significant mortality after 3 days of continuous exposure to treated wheat. Nine days after treatment, the median lethal doses (LD50) observed ranged from 127 to 235 mg kg−1.CONCLUSION: Comparison of these results with recommended rates for commercial insecticidal dusts suggests that inorganic nanostructured alumina may provide a cheap and reliable alternative for control of insect pests. This study expands the frontiers for nanoparticle‐based technologies in pest management. Further research is needed to identify its mode of action and its non‐target toxicity, and to determine the potential of other nanostructured materials as pest control options for insects. Copyright © 2010 Society of Chemical Industry
Residues of the herbicide fenoxaprop‐P‐ethyl, its agronomic safener isoxadifen‐ethyl and their metabolites in rice after field application
Authors: Lucini Luigi , Pietro Molinari Gian 
Published: February 2010

AbstractBACKGROUND: Fenoxaprop‐P‐ethyl is a herbicide used on cereals and in particular on rice, the degradation of which leads to several relevant metabolites. The herbicide is used together with an agronomic safener such as isoxadifen‐ethyl, which also generates some metabolites. The present work was aimed at developing and validating an analytical method for the determination of the above parent compounds and their main metabolites in the edible fractions of rice. Parent compounds were extracted in acetonitrile and determined by gas chromatography with a mass spectrometer detector, while metabolites were extracted in acetonitrile and analysed by liquid chromatography tandem mass spectrometry.RESULTS: The method was validated through recovery tests in rice straw, grain and plant: accuracy was in the range 76–86% and 90–103% for parent compounds and metabolites respectively. Precision, as relative standard deviation, was in the range 3–11% and 6–17% for parent compounds and metabolites respectively. The limit of detection was 0.01 mg kg−1 for each analyte, while the limit of quantification was set at 0.05 mg kg−1.CONCLUSION: The analytical method is suitable for quantitative determination of each analyte considered in rice commodities. Copyright © 2010 Society of Chemical Industry
The relationship between $I_{{\rm H}_{\rm \alpha } } /(I_{{\rm SiH}}^* )^2$ and crystalline volume fraction in microcrystalline silicon growth
Authors: Chantana Jakapan , Higuchi Takuya , Nagai Tomoyuki , Sasaki Shota , Sobajima Yasushi , Toyama Toshihiko , Sada Chitose , Matsuda Akihisa , Okamoto Hiroaki 
Published: February 2010

AbstractOptical‐emission‐intensity ratio of $I_{{\rm H}_{\rm \alpha } } /(I_{{\rm SiH}}^* )$ during film growth has been used as a simple indicator to predict crystallinity (crystal‐volume fraction: XC) in the resulting microcrystalline silicon (µc‐Si:H) thin films. The relationship between $I_{{\rm H}_{\rm \alpha } } /(I_{{\rm SiH}}^* )$ and XC has been checked under a wide variety of film‐preparation conditions including low‐deposition‐rate (<0.1 nm/s) and high‐deposition‐rate (>5 nm/s) cases. On the basis of theoretical consideration, we have proposed optical‐emission‐intensity ratio of $I_{{\rm H}_{\rm \alpha } } /(I_{{\rm SiH}}^* )^2 $ as a new indicator of XC during film growth of µc‐Si:H.
Field‐induced nematic phase in the spin ladder system with easy‐axis anisotropy
Authors: Sakai Tôru , Tonegawa Takashi , Okamoto Kiyomi 
Published: February 2010

AbstractThe spin ladder system with the easy‐axis anisotropy in magnetic field is theoretically investigated using the numerically exact diagonalization, the density matrix renormalization group (DMRG) and the finite‐size scaling analysis. It is found that the field‐induced nematic phase appears above the critical field. In addition, there exists another critical field at which the quantum phase transition from the nematic phase to the conventional field‐induced Tomonaga–Luttinger liquid (TLL) phase occurs. The phase diagram on the coupling anisotropy versus magnetization plane is given by the numerical diagonalization. Furthermore, a typical magnetization curve calculated by the DMRG is presented.
Observing the anisotropic optical response of the heavy‐fermion compound UNi2Al3
Authors: Ostertag Julia P. , Scheffler Marc , Dressel Martin , Jourdan Martin 
Published: February 2010

AbstractThe optical conductivity of heavy fermions can reveal fundamental properties of the charge carrier dynamics in these strongly correlated electron systems. Here we extend the conventional techniques of infrared optics on heavy fermions by measuring the transmission and phase shift of THz radiation that passes through a thin film of UNi2Al3, a material with hexagonal crystal structure. We deduce the optical conductivity in a previously not accessible frequency range, and furthermore we resolve the anisotropy of the optical response (parallel and perpendicular to the hexagonal planes). At frequencies around 7 cm−1, we find a strongly temperature‐dependent and anisotropic optical conductivity that – surprisingly – roughly follows the dc behavior.
Anisotropy of the low‐temperature magnetostriction of Sr3Ru2O7
Authors: Stingl C. , Perry R. S. , Maeno Y. , Gegenwart P. 
Published: February 2010

AbstractWe use high‐resolution capacitive dilatometry to study the low‐temperature linear magnetostriction of the bilayer ruthenate Sr3Ru2O7 as a function of magnetic field applied perpendicular to the ruthenium‐oxide planes ($B\parallel c$). The relative length change ${\rm \Delta }L(B)/L$ is detected either parallel or perpendicular to the c‐axis close to the metamagnetic region near B = 8 T. In both cases, clear peaks in the coefficient $\lambda (B) = {\rm d}({\rm \Delta }L/L)/{\rm d}B$ at three subsequent metamagnetic transitions are observed. For ${\rm \Delta }L \bot c$, the third transition at 8.1 T bifurcates at temperatures below 0.5 K. This is ascribed to the effect of an in‐plane uniaxial pressure of about 15 bar, unavoidable in the dilatometer, which breaks the original fourfold in‐plane symmetry.
Magnetotransport in the magnetic superconductor HoNi2B2C
Authors: Ohashi M. , Oomi G. , Cho B. K. , Canfield P. C. 
Published: February 2010

AbstractThe electrical resistivity and the magnetization of single crystalline HoNi2B2C have been measured at several magnetic fields. In the paramagnetic region, the magnetization is nicely reproduced by calculations that take the crystal electric field (CEF) into consideration. The magnetoresistance is negative at a wide temperature range, and is strongly dependent on the magnetization. It is interpreted by the reduction of spin‐disorder scattering as the moments are polarized.
Performance improvement in bucky gel actuators by chemical modifications of carbon nanotubes
Authors: Biso Maurizio , Ansaldo Alberto , Ricci Davide 
Published: February 2010

AbstractSingle walled carbon nanotubes functionalized with an aromatic diamine have been successfully used to prepare bucky gel layers by mixing with an imidazolium based ionic liquid, allowing to build bimorph actuators that significantly outperform those prepared by using the pristine or oxidized carbon nanotubes. The carbon nanotube gravimetric specific capacitance doubles, the actuator maximum operating frequency becomes five times higher and for same injected charge the strain reaches a fourfold increase. The origin of such dramatic effects is most probably due to an enhanced binding between the carbon nanotubes induced by their chemical modification. (© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Antiplasmodial and cytotoxic activity of phloroglucinol derivatives from Hypericum erectum thunb
Authors: Moon Hyung‐In 
Published: February 2010

AbstractThe chloroform extracts of whole plants of Hypericum erectum were investigated for antiplasmodial activity against chloroquine‐sensitive strains of Plasmodium falciparum. Five phloroglucinol derivatives, otogirin (1), otogirone (2), erectquione A (3), erectquione B (4), and erectquione C (5) were isolated from the whole plants of H. erectum. Also, five compounds were evaluated for in vitro antiplasmodial activities as well as their cytotoxic potential on SK‐OV‐3 cancer cell line cells. Compounds 2, 4 showed notable growth inhibitory activity against chloroquine‐sensitive strains of Plasmodium falciparum with IC50 values from 5.6 and 7.2 μM. This compound showed no significant cytotoxicity (IC50 > 150 μM) evaluated using SK‐OV‐3 cancer cell line cells. Copyright © 2010 John Wiley & Sons, Ltd.
The tocotrienol‐rich fraction from rice bran enhances cisplatin‐induced cytotoxicity in human mesothelioma H28 cells
Authors: Nakashima Keisuke , Virgona Nantiga , Miyazawa Mio , Watanabe Takashi , Yano Tomohiro 
Published: February 2010

AbstractResistance to chemotherapy (chemoresistance) is a serious problem in malignant mesothelioma, a highly aggressive neoplasm. Gamma‐tocotrienol (γ‐T3) can sensitize various cancerous cells to chemotherapeutic agents by inhibiting pathways that lead to treatment resistance. In this study, we investigated the modulating effect of tocotrienol‐rich fraction (TRF) from rice bran, which is abundant in γ‐T3, on chemoresistance in human MM H28 cells. TRF treatment caused a marked reduction in the viability of H28 cells in a dose‐dependent manner, while cisplatin treatment had no effect on the cells, indicating that H28 cells are resistant to cisplatin. A significant increase in cytotoxicity was observed in H28 cells treated with TRF, and this effect was enhanced by the combination treatment with cisplatin. The cytotoxic effect was closely related to the inhibition of phosphatidylinositol 3‐kinase (PI3K)‐AKT signaling. Inactivation of Akt signaling by TRF or the combination with cisplatin mitigated cisplatin‐induced activation of Akt, resulting in reducing the chemoresistance H28 cells to cisplatin. Reduced cell viability and attenuated chemoresistance of the H28 cells against cisplatin were also observed following the use of a PI3K inhibitor, LY294002. These results suggest that the combination therapy of cisplatin with TRF is a plausible strategy for achieving tolerance for the chemotherapeutic agent in MM therapy. Copyright © 2010 John Wiley & Sons, Ltd.
Four‐dimensional variational assimilation in the unstable subspace and the optimal subspace dimension
Authors: Trevisan Anna , D'Isidoro Massimo , Talagrand Olivier 
Published: February 2010

AbstractKey apriori information used in 4D‐Var is the knowledge of the system's evolution equations. In this article we propose a method for taking full advantage of the knowledge of the system's dynamical instabilities in order to improve the quality of the analysis. We present an algorithm for four‐dimensional variational assimilation in the unstable subspace (4D‐Var – AUS), which consists of confining in this subspace the increment of the control variable. The existence of an optimal subspace dimension for this confinement is hypothesized. Theoretical arguments in favour of the present approach are supported by numerical experiments in a simple perfect nonlinear model scenario. It is found that the RMS analysis error is a function of the dimension N of the subspace where the analysis is confined and is a minimum for N approximately equal to the dimension of the unstable and neutral manifold. For all assimilation windows, from 1 to 5 d, 4D‐Var – AUS performs better than standard 4D‐Var. In the presence of observational noise, the 4D‐Var solution, while being closer to the observations, is farther away from the truth. The implementation of 4D‐Var – AUS does not require the adjoint integration. Copyright © 2010 Royal Meteorological Society