bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phase I Clinical Trial of a Selective Inhibitor of CYP17, Abiraterone Acetate, Confirms That Castration-Resistant Prostate Cancer Commonly Remains Hormone Driven
Authors: Attard Gerhardt , Reid Alison H.M. , Yap Timothy A. , Raynaud Florence , Dowsett Mitch , Settatree Sarah , Barrett Mary , Parker Christopher , Martins Vanessa , Folkerd Elizabeth , Clark Jeremy , Cooper Colin S. , Kaye Stan B. , Dearnaley David , Lee Gloria , de Bono Johann S. 
Published: July 2008

Purpose Studies indicate that castration-resistant prostate cancer (CRPC) remains driven by ligand-dependent androgen receptor (AR) signaling. To evaluate this, a trial of abiraterone acetate—a potent, selective, small-molecule inhibitor of cytochrome P (CYP) 17, a key enzyme in androgen synthesis—was pursued. Patients and Methods Chemotherapy-naïve men (n = 21) who had prostate cancer that was resistant to multiple hormonal therapies were treated in this phase I study of once-daily, continuous abiraterone acetate, which escalated through five doses (250 to 2,000 mg) in three-patient cohorts. Results Abiraterone acetate was well tolerated. The anticipated toxicities attributable to a syndrome of secondary mineralocorticoid excess—namely hypertension, hypokalemia, and lower-limb edema—were successfully managed with a mineralocorticoid receptor antagonist. Antitumor activity was observed at all doses; however, because of a plateau in pharmacodynamic effect, 1,000 mg was selected for cohort expansion (n = 9). Abiraterone acetate administration was associated with increased levels of adrenocorticotropic hormone and steroids upstream of CYP17 and with suppression of serum testosterone, downstream androgenic steroids, and estradiol in all patients. Declines in prostate-specific antigen ≥ 30%, 50%, and 90% were observed in 14 (66%), 12 (57%), and 6 (29%) patients, respectively, and lasted between 69 to ≥ 578 days. Radiologic regression, normalization of lactate dehydrogenase, and improved symptoms with a reduction in analgesic use were documented. Conclusion CYP17 blockade by abiraterone acetate is safe and has significant antitumor activity in CRPC. These data confirm that CRPC commonly remains dependent on ligand-activated AR signaling.
Smectic A Formation by Twin Dimers Assuming U-shaped Conformation
Authors: Naito Yu , Ishige Ryohei , Itoh Manabu , Tokita Masatoshi , Watanabe Junji 
Published: July 2008

Abstract
Twin dimers with 3-methylpentane spacers behave as U-shaped (folding) molecules if the carbon number of alkyl tail group is longer than 12 and form an SA phase. This behavior is in contrast to that in dimers with linear pentane spacers which assume extended conformation and form the antiferroelectric SCAb. Folding of twin molecules, hence, is another way to accommodate tail groups fairly longer than the spacers, suggesting new potentiality in spontaneous molecular organization.
FTIR spectroscopy in combination with principal component analysis or cluster analysis as a tool to distinguish beech (Fagus sylvatica L.) trees grown at different sites
Authors: Rana Rumana , Müller Günter , Naumann Annette , Polle Andrea 
Published: July 2008

Abstract
FTIR spectroscopy was used to distinguish between beech (Fagus sylvatica L.) trees grown at five different sites; one in middle Germany close to Göttingen (forest district Reinhausen), three located in the southwest (two in Rhineland-Palatinate: forest districts Saarburg and Hochwald, and one in Luxembourg), and one in North-Rhine Westfalia. Detailed investigation of the spectra in the fingerprint region (1800–600 cm-1) revealed 16 distinct peaks and shoulders, most of which were assignable to wavenumbers previously shown to represent wood compounds. Differences in peak heights and peak ratios indicated differences in wood composition of beech trees from different sites. To determine if the wood of individual trees could be distinguished, principal component analysis (PCA) and cluster analysis were performed using FTIR spectra as input data. With both PCA and cluster analysis, trees from four of the five different sites were separated. It was not possible to distinguish between trees from Saarburg and Hochwald, where similar edaphic and climatic conditions exist, while wood spectra from trees from all other areas clearly segregated. Wood collected at different positions in the stem (bottom, crown, center and outer year rings) of trees grown at the same site was not distinguishable. Therefore, FTIR spectral analysis in combination with multivariate statistical methods can be used to distinguish wood of trees from different growth habitats. Extension of this method to other species may be of great interest for wood certification, as it may be possible to distinguish wood, of a given species, originating from different regions.
Thyroid B-flow twinkling sign: a new feature of papillary cancer
Authors: Brunese Luca , Romeo Antonio , Iorio Sergio , Napolitano Giuseppina , Fucili Stefano , Zeppa Pio , Vallone Gianfranco , Lombardi Gaetano , Bellastella Antonio , Biondi Bernadette , Sodano Antonio 
Published: July 2008

BackgroundMicrocalcifications (aggregated with psammoma bodies), detected by ultrasound (US), are the most specific feature of papillary thyroid cancer (PTC). Using B-flow imaging (BFI), we identified a new sign (the twinkling sign; BFI-TS) in ‘suspect’ PTC nodules, which appeared to be generated by microcalcifications.ObjectiveTo evaluate whether the BFI-TS was predictive of malignancy, we correlated the BFI-TS with the results of fine needle aspiration cytology and histology.DesignCross-sectional cohort study from September 2006 to April 2008.SettingDepartment of Radiology and Endocrinology, University of Naples Federico II, and Department of Endocrinology, Second University of Naples.PatientsA total of 306 consecutive patients with 539 thyroid nodules >8 mm in diameter.Main outcome measureUS and BFI examinations were performed with the Logiq 9 system (General Electric Company, Milan, Italy); all patients underwent cytological examination.ResultsCytology revealed 455 (84.4%) benign nodules and 84 (15.6%) malignant nodules; the latter were confirmed by postsurgical histological examination (76 cases of PTC, 7 follicular carcinoma, and 1 Hürthle cell carcinoma). All suspect nodules, namely, nodules with potential predictors of thyroid malignancy (e.g., microcalcifications and intra-nodal vascularity), were analyzed by cytology or histology (or both). Of 84, 68 (80.9%) of malignant nodules had ≥4 or more BFI-TSs in at least one scan versus only 12 of 455 (2.6%) of benign lesions.ConclusionsOur results indicate that the BFI-TS could be a reliable diagnostic technique in the management of suspect thyroid nodules.
Initial kinetics of the direct sulfation of limestone
Authors: Hu Guilin , Shang Lei , Dam‐Johansen Kim , Wedel Stig , Hansen Jens Peter 
Published: July 2008

AbstractThe initial kinetics of direct sulfation of Faxe Bryozo, a porous bryozoan limestone was studied in the temperature interval from 873 to 973 K in a pilot entrained flow reactor with very short reaction times (between 0.1 and 0.6 s). The initial conversion rate of the limestone—for conversions less than 0.3%—was observed to be significantly promoted by higher SO2 concentrations and lower CO2 concentrations, whereas O2 showed negligible influence. A mathematical model for the sulfation of limestone involving chemical reaction at calcite grain surfaces and solid‐state diffusion of carbonate ions in calcite grains is established. The validity of the model is limited to the initial sulfation period, in which nucleation of the solid product calcium sulphate is not started. This theoretical reaction‐diffusion model gives a good simulation of the initial kinetics of the direct sulfation of Faxe Bryozo. The intrinsic rate of the direct sulfation of the limestone is estimated to have an activation energy of about 25 kJ/mol and reaction orders of about 0.9 and −0.75 for SO2 and CO2, respectively. The diffusivity of carbonate ions in the surface layer of the calcite grain is estimated to be about three orders of magnitude higher than the diffusivity of carbonate ions in the inner lattice of calcite grain and have an activation energy of about 202 kJ/mol. © 2008 American Institute of Chemical Engineers AIChE J, 2008
Photometric membership and metallicities of red giant candidates in selected open clusters
Authors: Clariá J.J. , Piatti A.E. , Mermilliod J.‐C. , Palma T. 
Published: July 2008

AbstractAs part of a long‐term project to determine abundances and astrophysical properties of evolved red stars in open clusters, we present high‐precision DDO photoelectric observations for a sample of 33 red giant candidates projected in the fields of nine Galactic open clusters. These data are supplemented with UBV photoelectric photometry of 24 of these stars as well as with CORAVEL radial‐velocity observations for 13 red giant candidates in four of the clusters. We also present Washington photoelectric photometry of a small sample of red giant candidates of the open cluster Ruprecht 97. The likelihood of cluster membership for each star photometrically observed and for 23 additional red giant candidates with UBV and DDO data available in the literature, is evaluated by using two independent photometric criteria. Nearly 82% of the analysed stars are found to have a high probability of being cluster giants. Photometric membership probabilities show very good agreement with those obtained from CORAVEL radial velocities. While E (B –V) colour excesses were determined from combined B – V and DDO colours, calibrations of the DDO system were used to derive MK spectral types, effective temperatures and metallicities. The derived DDO metallicities range between values typical of moderately metal‐poor clusters ([Fe/H] = –0.19) to moderately metal‐rich ([Fe/H] = 0.25) ones. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Possible third body effects in the period changes of four Algol binaries: RY Aqr, SZ Her, RV Lyr and V913 Oph
Authors: Soydugan F. 
Published: July 2008

AbstractAn investigation of the orbital period changes of the neglected eclipsing binaries, RY Aqr, SZ Her, RV Lyr and V913 Oph, is presented based on all published minima times. Although the explanation of magnetic activity on the surface of the secondaries of the studied Algols is still open, the preferred light‐time effect due to the unseen components around the systems seems more plausible in explaining the tilted sinusoidal variations with relatively high‐amplitudes. The minimal mass values of possible tertiary components have been estimated to be about 1.06, 0.25, 0.78 and 2.85 M⊙ for RY Aqr, SZ Her, RV Lyr and V913 Oph, respectively and the results indicate that their contributions to the total light of the eclipsing pairs are measurable with high accuracy photometric and spectroscopic data, if they exist. Applegate's (1992) model has been discussed as an alternative mechanism assuming that the cooler components have magnetic cycles. It is found that the model parameters of RY Aqr and V913 Oph are consistent with the required values in Applegate's model. In addition to the first detailed orbital study on these systems, a statistical survey on the character of the O – C variations of classical Algols has revealed that about 50 percent of the systems show cyclic behavior. This means that the presence of possible third bodies around classical Algols should be tested with careful analysis using new data. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Photometric study of 9 doubtful open clusters
Authors: Maciejewski G. , Niedzielski A. 
Published: July 2008

AbstractWe present results of a photometric investigation of 9 poorly studied apparent open clusters. While the aim of our survey was to determine structural and astrophysical parameters for these objects, they were found not to be physical groups of stars. BV wide‐field CCD photometry combined with the near‐infrared JHKS data from the 2MASS and proper motions were used to study their nature. Detailed analysis of radial density profiles, morphology of decontaminated colourmagnitude diagrams, and proper motion distributions indicate that these stellar ensembles are projective chance alignments of physically unrelated stars. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Comparative transcriptome analysis to unveil genes affecting recombinant protein productivity in mammalian cells
Authors: Yee Joon Chong , Gerdtzen Ziomara P. , Hu Wei‐Shou 
Published: July 2008

AbstractLow temperature culture (33°C) has been shown to enhance the specific productivity of recombinant antibodies in Chinese hamster ovary (CHO) cells but did not affect antibody productivity in hybridoma (MAK) cells. We probed the transcriptional response of both cells undergoing temperature shift using cDNA microarrays. Among the orthologous gene probes, common trends in the expression changes between CHO and MAK are not prominent. Instead, many transcriptional changes were specific to only one cell line. Notably, oxidative phosphorylation and ribosomal genes were downregulated in MAK but not in CHO. Conversely, several protein trafficking genes and cytoskeleton elements were upregulated in CHO but remained unchanged in MAK. Interestingly, at 33°C, immunoglobulin heavy and light chain showed no significant changes in CHO, but the immunoglobulin light chain was downregulated in MAK. Overall, a clear distinction in the transcriptional response to low temperature was seen in the two cell lines. To further elucidate the set of genes responsible for increased antibody productivity, the expression data of low temperature cultures was compared to that of butyrate treatment which increased specific antibody productivity in both cell lines. Genes which are commonly differentially expressed under conditions that increased productivity are likely to reflect functional classes that are important in the productivity changes. This comparative transcriptome analysis suggests that vesicle trafficking, endocytosis and cytoskeletal elements are involved in increased specific antibody productivity. Biotechnol. Bioeng. 2009;102: 246–263. © 2008 Wiley Periodicals, Inc.
Bioreactor strategies for improving production yield and functionality of a recombinant human protein in transgenic tobacco cell cultures
Authors: Huang Ting‐Kuo , Plesha Michael A. , Falk Bryce W. , Dandekar Abhaya M. , McDonald Karen A. 
Published: July 2008

AbstractPlant cell culture production of recombinant products offers a number of advantages over traditional eukaryotic expression systems, particularly if the product can be targeted to and purified from the cell culture broth. However, one of the main obstacles is product degradation by proteases that are produced during cell culture, and/or the loss of biological activity of secreted (extracellular) products as a result of alteration in the protein conformation. Because proteolysis activity and target protein stability can be significantly influenced by culture conditions, it is important to evaluate bioprocess conditions that minimize these effects. In this study, a bioreactor strategy using a protocol involving pH adjustment and medium exchange during plant cell culture is proposed for improving the production of functional recombinant α1‐antitrypsin (rAAT), a human blood protein, produced using several alternative expression systems, including a Cauliflower mosaic virus (CaMV) 35S constitutive promoter expression system, a chemically inducible, estrogen receptor‐based promoter (XVE) expression system, and a novel Cucumber mosaic virus (CMV) inducible viral amplicon (CMViva) expression system developed by our group. We have demonstrated that higher medium pH help reduce protease activity derived from cell cultures and improve the inherent stability of human AAT protein as well. This strategy resulted in a fourfold increase in the productivity of extracellular functional rAAT (100 µg/L) and a twofold increase in the ratio of functional rAAT to total rAAT (48%) in transgenic N. benthamiana cell cultures using a chemically inducible viral amplicon expression system. Biotechnol. Bioeng. 2009;102: 508–520. © 2008 Wiley Periodicals, Inc.
Reduction of a set of elementary modes using yield analysis
Authors: Song Hyun‐Seob , Ramkrishna Doraiswami 
Published: July 2008

AbstractThis article proposes a new concept termed “yield analysis” (YA) as a method of extracting a subset of elementary modes (EMs) essential for describing metabolic behaviors. YA can be defined as the analysis of metabolic pathways in yield space where the solution space is a bounded convex hull. Two important issues arising in the analysis and modeling of a metabolic network are handled. First, from a practical sense, the minimal generating set spanning the yield space is recalculated. This refined generating set excludes all the trivial modes with negligible contribution to convex hull in yield space. Second, we revisit the problem of decomposing the measured fluxes among the EMs. A consistent way of choosing the unique, minimal active modes among a number of possible candidates is discussed and compared with two other existing methods, that is, those of Schwartz and Kanehisa (Schwartz and Kanehisa, 2005. Bioinformatics 21: 204–205) and of Provost et al. (Provost et al., 2007. Proceedings of the 10th IFAC Symposium on Computer Application in Biotechnology, 321–326). The proposed idea is tested in a case study of a metabolic network of recombinant yeasts fermenting both glucose and xylose. Due to the nature of the network with multiple substrates, the flux space is split into three independent yield spaces to each of which the two‐staged reduction procedure is applied. Through a priori reduction without any experimental input, the 369 EMs in total was reduced to 35 modes, which correspond to about 91% reduction. Then, three and four modes were finally chosen among the reduced set as the smallest active sets for the cases with a single substrate of glucose and xylose, respectively. It should be noted that the refined minimal generating set obtained from a priori reduction still provides a practically complete description of all possible states in the subspace of yields, while the active set covers only a specific set of experimental data. Biotechnol. Bioeng. 2009;102: 554–568. © 2008 Wiley Periodicals, Inc.
A comparative study of awareness methods for peer‐to‐peer distributed virtual environments
Authors: Rueda S. , Morillo P. , Orduña J. M. 
Published: July 2008

AbstractThe increasing popularity of multi‐player online games is leading to the widespread use of large‐scale Distributed Virtual Environments (DVEs) nowadays. In these systems, peer‐to‐peer (P2P) architectures have been proposed as an efficient and scalable solution for supporting massively multi‐player applications. However, the main challenge for P2P architectures consists of providing each avatar with updated information about which other avatars are its neighbors. This problem is known as the awareness problem. In this paper, we propose a comparative study of the performance provided by those awareness methods that are supposed to fully solve the awareness problem. This study is performed using well‐known performance metrics in distributed systems. Moreover, while the evaluations shown in the literature are performed by executing P2P simulations on a single (sequential) computer, this paper evaluates the performance of the considered methods on actually distributed systems. The evaluation results show that only a single method actually provides full awareness to avatars. This method also provides the best performance results. Copyright © 2008 John Wiley & Sons, Ltd.
Exact solution of vibration problems of frame structures
Authors: Ma Haitao 
Published: July 2008

AbstractAlthough exact solutions for linear static analysis of most frame structures can be obtained by the finite element method, it is very difficult to get exact solutions for free vibration and harmonic analyses for non‐trivial cases. This paper extends an earlier study on exact solutions of axial vibration problems of elastic bars to dynamic analyses of elastic frame structures. New shape functions for the transverse displacement field are constructed by using the homogeneous governing equations and then a novel beam element is formulated. Combining the new (bending) beam element and the one developed earlier for elastic bars yields a new element for general frame structures. The new frame element can be used to get exact solutions for both natural frequency and undamped harmonic analyses of frame structures. Illustrative examples are presented to demonstrate the effectiveness of the new element and the algorithm. Copyright © 2008 John Wiley & Sons, Ltd.
Improving performance of optimized kernels through fast instantiations of templates
Authors: Khan Minhaj Ahmad , Charles H.‐P. , Barthou D. 
Published: July 2008

AbstractTo fully exploit the instruction‐level parallelism offered by modern processors, compilers need the necessary information available during the execution of the program. This advocates for iterative or dynamic compilation. Unfortunately, dynamic compilation is suitable only for applications where the cost of compilation may be amortized by multiple invocations of the same code. Similarly, the cost of iterative compilation makes it impractical to be widely used for performance improvement. In this article, we suggest a novel approach for improving the performance of mathematical kernels through fast instantiations of templates. Optimized templates are generated at static compile time with a limited number of compilations. The initial instantiations of these templates are performed at static compile time, and the runtime instantiations are performed with a very small overhead through specialized data, requiring no computations at runtime. It represents an effective solution in terms of reduced overhead incurring at static compile time and dynamic compile time. The experiments have been performed on an Itanium‐II architecture using highly optimized kernels ofATLASandFFTWwithiccandgcccompilers. Copyright © 2008 John Wiley & Sons, Ltd.
Writing productive stencil codes with overlapped tiling
Authors: Guo Jia , Bikshandi Ganesh , Fraguela Basilio B. , Padua David 
Published: July 2008

AbstractStencil computations constitute the kernel of many scientific applications. Tiling is often used to improve the performance of stencil codes for data locality and parallelism. However, tiled stencil codes typically require shadow regions, whose management becomes a burden to programmers. In fact, it is often the case that the code required to manage these regions, and in particular their updates, is much longer than the computational kernel of the stencil. As a result, shadow regions usually impact programmers' productivity negatively. In this paper, we describeoverlapped tiling, a construct that supports shadow regions in a convenient, flexible and efficient manner in the context of the hierarchically tiled array (HTA) data type. The HTA is a class designed to express algorithms with a high degree of parallelism and/or locality as naturally as possible in terms of tiles. We discuss the syntax and implementation of overlapped HTAs as well as our experience in rewriting parallel and sequential codes using them. The results have been satisfactory in terms of both productivity and performance. For example, overlapped HTAs reduced the number of communication statements in non‐trivial codes by 78% on average while speeding them up. We also examine different implementation options and compare overlapped HTAs with previous approaches. Copyright © 2008 John Wiley & Sons, Ltd.