bluuebunny/crossref_metadata_2025_split huggingface dataset:
Systematic screening and characterization of the major bioactive components of Poria cocos and their metabolites in rats by LC‐ESI‐MSn
Authors: Ling Yun , Chen Mingcang , Wang Ke , Sun Zhaolin , Li Zhixiong , Wu Bin , Huang Chenggang 
Published: December 2011

ABSTRACTPoria cocos is a well‐known medicinal plant widely used in China and other East Asian countries owing to its various therapeutic effects. However, the bioactive constituents responsible for the pharmacological effects of Poria cocos and their metabolites in vivo are still unclear to date. The aim of the present study was to develop a practical method based on the combined use of the liquid chromatography coupled with electrospray ionization multistage tandem mass spectrometry (LC‐ESI‐MSn) for the comprehensive and systematic separation and characterization of the bioactive constituents of Poria cocos extract and their metabolites in rats. Based on the proposed strategy, a total of 34 compounds were characterized from the extract of Poria cocos. Among them, eight were unambiguously identified by comparing their retention times and mass spectra with those of reference standards, and 26 were tentatively identified on the basis of their MSn fragmentation behaviors and molecular weight information from literatures. In vivo, seven compounds were successfully detected in rat urine whereas one was found in rat plasma. This study proposed a series of potential bioactive components and provided helpful chemical information for further research on the action mechanism of traditional Chinese medicine. Copyright © 2011 John Wiley & Sons, Ltd.
Development and validation of a rapid LC‐MS/MS method for the determination of JCC76, a novel antitumor agent for breast cancer, in rat plasma and its application to a pharmacokinetics study
Authors: Cai Xiaohan , Zhong Bo , Su Bin , Xu Songlin , Guo Baochuan 
Published: December 2011

ABSTRACTJCC76 is a novel nimesulide analog that selectively inhibits the human epidermal growth factor receptor 2 (HER2) overexpressing breast cancer cell proliferation and tumor progression. To support further pharmacological and toxicological studies of JCC76, a novel and rapid method using liquid chromatography and electrospray ionization tandem mass spectrometry (LC‐ESI‐MS/MS) has been developed and validated for the quantification of the compound in rat plasma. A C18 column was used for chromatographic separation, and the mobile phase was aqueous ammonium formate (pH 3.7; 5 mm)–methanol (1:9, v/v) with an isocratic elution. With a simple liquid–liquid extraction procedure using the mixture of methyl tert‐butyl ether–hexane (1:2, v/v), the mean extraction efficiency of JCC76 in rat plasma was determined as 89.5–97.3% and no obvious matrix effect was observed. This method demonstrated a linear calibration range from 0.3 to 100 ng/mL for JCC76 in rat plasma and a small volume of sample consumption. The intra‐ and inter‐assay accuracy and precision were within ±10%. The pharmacokinetics of JCC76 was also profiled using this validated method in rats. In conclusion, this rapid and sensitive method has been proven to effectively quantify JCC76 for pharmacokinetics study. Copyright © 2011 John Wiley & Sons, Ltd.
Rhodium‐Catalyzed Asymmetric Hydrogenation of Olefins with PhthalaPhos, a New Class of Chiral Supramolecular Ligands
Authors: Pignataro Luca , Boghi Michele , Civera Monica , Carboni Stefano , Piarulli Umberto , Gennari Cesare 
Published: December 2011

AbstractA library of 19 binol‐derived chiral monophosphites that contain a phthalic acid diamide group (PhthalaPhos) has been designed and synthesized in four steps. These new ligands were screened in the rhodium‐catalyzed enantioselective hydrogenation of prochiral dehydroamino esters and enamides. Several members of the library showed excellent enantioselectivity with methyl 2‐acetamido acrylate (6 ligands gave >97 % ee), methyl (Z)‐2‐acetamido cinnamate (6 ligands gave >94 % ee), and N‐(1‐phenylvinyl)acetamide (9 ligands gave >95 % ee), whilst only a few representatives afforded high enantioselectivities for challenging and industrially relevant substrates N‐(3,4‐dihydronaphthalen‐1‐yl)‐acetamide (96 % ee in one case) and methyl (E)‐2‐(acetamidomethyl)‐3‐phenylacrylate (99 % ee in one case). In most cases, the new ligands were more active and more stereoselective than their structurally related monodentate phosphites (which are devoid of functional groups that are capable of hydrogen‐bonding interactions). Control experiments and kinetic studies were carried out that allowed us to demonstrate that hydrogen‐bonding interactions involving the diamide group of the PhthalaPhos ligands strongly contribute to their outstanding catalytic properties. Computational studies carried out on a rhodium precatalyst and on a conceivable intermediate in the hydrogenation catalytic cycle shed some light on the role played by hydrogen bonding, which is likely to act in a substrate‐orientation effect.
An automated analysis of highly complex flow cytometry‐based proteomic data
Authors: Stuchlý Jan , Kanderová Veronika , Fišer Karel , Černá Daniela , Holm Anders , Wu Weiwei , Hrušák Ondřej , Lund‐Johansen Fridtjof , Kalina Tomáš 
Published: December 2011

AbstractThe combination of color‐coded microspheres as carriers and flow cytometry as a detection platform provides new opportunities for multiplexed measurement of biomolecules. Here, we developed a software tool capable of automated gating of color‐coded microspheres, automatic extraction of statistics from all subsets and validation, normalization, and cross‐sample analysis. The approach presented in this article enabled us to harness the power of high‐content cellular proteomics. In size exclusion chromatography‐resolved microsphere‐based affinity proteomics (Size‐MAP), antibody‐coupled microspheres are used to measure biotinylated proteins that have been separated by size exclusion chromatography. The captured proteins are labeled with streptavidin phycoerythrin and detected by multicolor flow cytometry. When the results from multiple size exclusion chromatography fractions are combined, binding is detected as discrete reactivity peaks (entities). The information obtained might be approximated to a multiplexed western blot. We used a microsphere set with >1,000 subsets, presenting an approach to extract biologically relevant information. The R‐project environment was used to sequentially recognize subsets in two‐dimensional space and gate them. The aim was to extract the median streptavidin phycoerythrin fluorescence intensity for all 1,000+ microsphere subsets from a series of 96 measured samples. The resulting text files were subjected to algorithms that identified entities across the 24 fractions. Thus, the original 24 data points for each antibody were compressed to 1–4 integrated values representing the areas of individual antibody reactivity peaks. Finally, we provide experimental data on cellular protein changes induced by treatment of leukemia cells with imatinib mesylate. The approach presented here exemplifies how large‐scale flow cytometry data analysis can be efficiently processed to employ flow cytometry as a high‐content proteomics method. © 2011 International Society for Advancement of Cytometry
Phenanthroline‐ and Terpyridine‐Substituted Tetralactam Macrocycles: A Facile Route to Rigid Di‐ and Trivalent Receptors and Interlocked Molecules
Authors: Dzyuba Egor V. , Baytekin Bilge , Sattler Dominik , Schalley Christoph A. 
Published: December 2011

AbstractBromo‐substituted Hunter/Vögtle‐type tetralactam macrocycles (TLMs) represent key intermediates for the attachment of terpyridyl and phenanthroline metal binding sites through cross‐coupling reactions. From these monovalent precursors, metal complexes can easily be obtained that present the macrocycles in a multivalent fashion. Depending on the nature of the metal ion, the properties of the complexes can be tuned with respect to valency (e.g., phen‐TLM + CuI: divalent, phen‐TLM + FeII: trivalent) and lability against TLM ligand exchange (e.g., CuI: slow, but reversible exchange, RuIICl2: kinetically inert).
Evaluation of the performance of a micro gas turbine cogeneration system in a sewage treatment facility: Optimized configuration of a cogeneration system
Authors: Basrawi Firdaus , Yamada Takanobu , Nakanishi Kimio 
Published: December 2011

AbstractIn this study, efficient configuration of a biogas‐fuelled cogeneration system (CGS) in a sewage treatment facility was investigated. The efficient configuration of the CGS was clarified on the basis of the relationship between exhaust heat recovery efficiency (ηehr) of the CGS and the ratio of yearly average heat demand to yearly average biogas production of the facility (Qh.d/Qb.p). The CGS was assumed to be used under Qh.d/Qb.p<ηehr,Qh.d/Qb.p≈ηehr, and Qh.d/Qb.p>ηehr conditions. It was found that although the CGS was able to cover total heat demand of the facility by only consuming biogas produced, from the point of view of energy utilization, reduction of unutilized biogas and reduction of electricity demand efficiencies, the most efficient CGS was obtained under the Qh.d/Qb.p≈ηehr condition. Under the Qh.d/Qb.p≈ηehr condition, energy utilization, reduction of unutilized biogas, and reduction of electrical demand efficiencies were 0.64, 0.99, and 0.32, respectively, whereas under the Qh.d/Qb.p<ηehr and Qh.d/Qb.p>ηehr conditions, energy utilization, reduction of unutilized biogas, and reduction of electrical demand efficiencies were in ranges of 0.56–0.64, 0.43–0.99, and 0.16–0.20, respectively. A more efficient system can be obtained if a CGS with lower ηehr such as a fuel cell is used under the Qh.d/Qb.p<ηehr condition and if a CGS with higher ηehr such as a steam turbine is used under the Qh.d/Qb.p>ηehr condition. © 2011 Wiley Periodicals, Inc. Heat Trans Asian Res; Published online in Wiley Online Library (wileyonlinelibrary.com/journal/htj). DOI 10.1002/htj.20389
Promyelocytic leukemia nuclear bodies support a late step in DNA double‐strand break repair by homologous recombination
Authors: Yeung Percy Luk , Denissova Natalia G. , Nasello Cara , Hakhverdyan Zhanna , Chen J. Don , Brenneman Mark A. 
Published: December 2011

AbstractThe PML protein and PML nuclear bodies (PML‐NB) are implicated in multiple cellular functions relevant to tumor suppression, including DNA damage response. In most cases of acute promyelocytic leukemia, the PML and retinoic acid receptor alpha (RARA) genes are translocated, resulting in expression of oncogenic PML‐RARα fusion proteins. PML‐NB fail to form normally, and promyelocytes remain in an undifferentiated, abnormally proliferative state. We examined the involvement of PML protein and PML‐NB in homologous recombinational repair (HRR) of chromosomal DNA double‐strand breaks. Transient overexpression of wild‐type PML protein isoforms produced hugely enlarged or aggregated PML‐NB and reduced HRR by ∼2‐fold, suggesting that HRR depends to some extent upon normal PML‐NB structure. Knockdown of PML by RNA interference sharply attenuated formation of PML‐NB and reduced HRR by up to 20‐fold. However, PML‐knockdown cells showed apparently normal induction of H2AX phosphorylation and RAD51 foci after DNA damage by ionizing radiation. These findings indicate that early steps in HRR, including recognition of DNA double‐strand breaks, initial processing of ends, and assembly of single‐stranded DNA/RAD51 nucleoprotein filaments, do not depend upon PML‐NB. The HRR deficit in PML‐depleted cells thus reflects inhibition of later steps in the repair pathway. Expression of PML‐RARα fusion proteins disrupted PML‐NB structure and reduced HRR by up to 10‐fold, raising the possibility that defective HRR and resulting genomic instability may figure in the pathogenesis, progression and relapse of acute promyelocytic leukemia. J. Cell. Biochem. 113: 1787–1799, 2012. © 2011 Wiley Periodicals, Inc.
Tolfenamic acid inhibits neuroblastoma cell proliferation and induces apoptosis: A novel therapeutic agent for neuroblastoma
Authors: Eslin Don , Sankpal Umesh T. , Lee Chris , Sutphin Robert M. , Maliakal Pius , Currier Erika , Sholler Giselle , Khan Moeez , Basha Riyaz 
Published: December 2011

AbstractCurrent therapeutic options for recurrent neuroblastoma have poor outcomes that warrant the development of novel therapeutic strategies. Specificity protein (Sp) transcription factors regulate several genes involved in cell proliferation, survival, and angiogenesis. Sp1 regulates genes believed to be important determinants of the biological behavior of neuroblastoma. Tolfenamic acid (TA), a non‐steroidal anti‐inflammatory drug, is known to induce the degradation of Sp proteins and may serve as a novel anti‐cancer agent. The objective of this investigation was to examine the anti‐cancer activity of TA using established human neuroblastoma cell lines. We tested the anti‐proliferative effect of TA using SH‐SY5Y, CHLA90, LA1 55n, SHEP, Be2c, CMP 13Y, and SMS KCNR cell lines. Cells were treated with TA (0/25/50/100 µM) and cell viability was measured at 24, 48, and 72 h post‐treatment. Selected neuroblastoma cell lines were treated with 50 µM TA for 24 and 48 h and tested for cell apoptosis using Annexin‐V staining. Caspase activity was measured with caspase 3/7 Glo kit. Cell lysates were prepared and the expression of Sp1, survivin, and c‐PARP were evaluated through Western blot analysis. TA significantly inhibited the growth of neuroblastoma cells in a dose/time‐dependent manner and significantly decreased Sp1 and survivin expression. Apart from cell cycle (G0/G1) arrest, TA caused significant increase in the apoptotic cell population, caspase 3/7 activity, and c‐PARP expression. These results show that TA effectively inhibits neuroblastoma cell growth potentially through suppressing mitosis, Sp1, and survivin expression, and inducing apoptosis. These results show TA as a novel therapeutic agent for neuroblastoma. © 2011 Wiley Periodicals, Inc.
Polymorphisms in GSTM1 and XPD genes predict clinical outcome in advanced oral cancer patients treated with postoperative radiotherapy
Authors: Mahimkar Manoj B. , Samant Tanuja A. , Kannan Sadhana , Tulsulkar Jatin , Pai Prathamesh S. , Anantharaman Devasena 
Published: December 2011

AbstractPolymorphisms in metabolic and DNA repair genes may alter protein function, consequently affecting patients' response to chemo/radiotherapy. We retrospectively assessed whether polymorphisms of glutathione‐S‐transferase genes GSTM1 (deletion), GSTT1 (deletion), GSTP1 (Ile105Val, rs1695), and DNA repair genes hOGG1 (Ser326Cys, rs1052133), XRCC1 (Arg194Trp, rs1799782, and Arg399Gln, rs25487), XPD (Asp312Asn, rs1799793, and Lys751Gln, rs13181) can predict clinical outcome in 187 oral squamous cell carcinoma patients treated with postoperative radiotherapy. The Cox proportional hazards model was used to evaluate the role of polymorphic genotypes on relapse‐free (RFS) and disease‐specific (DSS) survival. Deletion polymorphism of GSTM1 gene was significantly associated with DSS. The rs1799793 variant allele showed significant protection in both DSS and RFS. Significant increase in RFS but not in DSS was observed with polymorphic rs13181. The combined analysis of GSTM1 and XPD polymorphisms revealed favorable effect on survival. GSTM1 and XPD variant alleles, independently as well as in combination may serve as important predictors of clinical outcome in radiotherapy‐treated OSCC patients. © 2011 Wiley Periodicals, Inc.
Implementation and assessment of diffusion‐weighted partial Fourier readout‐segmented echo‐planar imaging
Authors: Frost Robert , Porter David A. , Miller Karla L. , Jezzard Peter 
Published: December 2011

AbstractSingle‐shot echo‐planar imaging has been used widely in diffusion magnetic resonance imaging due to the difficulties in correcting motion‐induced phase corruption in multishot data. Readout‐segmented EPI has addressed the multishot problem by introducing a two‐dimensional nonlinear navigator correction with online reacquisition of uncorrectable data to enable acquisition of high‐resolution diffusion data with reduced susceptibility artifact and T*2 blurring. The primary shortcoming of readout‐segmented EPI in its current form is its long acquisition time (longer than similar resolution single‐shot echo‐planar imaging protocols by approximately the number of readout segments), which limits the number of diffusion directions. By omitting readout segments at one side of k‐space and using partial Fourier reconstruction, readout‐segmented EPI imaging times could be reduced. In this study, the effects of homodyne and projection onto convex sets reconstructions on estimates of the fractional anisotropy, mean diffusivity, and diffusion orientation in fiber tracts and raw T2‐ and trace‐weighted signal are compared, along with signal‐to‐noise ratio results. It is found that projections onto convex sets reconstruction with 3/5 segments in a 2 mm isotropic diffusion tensor image acquisition and 9/13 segments in a 0.9 × 0.9 × 4.0 mm3 diffusion‐weighted image acquisition provide good fidelity relative to the full k‐space parameters. This allows application of readout‐segmented EPI to tractography studies, and clinical stroke and oncology protocols. Magn Reson Med, 2012. © 2011 Wiley‐Liss, Inc.
Denoising sparse images from GRAPPA using the nullspace method
Authors: Weller Daniel S. , Polimeni Jonathan R. , Grady Leo , Wald Lawrence L. , Adalsteinsson Elfar , Goyal Vivek K. 
Published: December 2011

AbstractTo accelerate magnetic resonance imaging using uniformly undersampled (nonrandom) parallel imaging beyond what is achievable with generalized autocalibrating partially parallel acquisitions (GRAPPA) alone, the DEnoising of Sparse Images from GRAPPA using the Nullspace method is developed. The trade‐off between denoising and smoothing the GRAPPA solution is studied for different levels of acceleration. Several brain images reconstructed from uniformly undersampled k‐space data using DEnoising of Sparse Images from GRAPPA using the Nullspace method are compared against reconstructions using existing methods in terms of difference images (a qualitative measure), peak‐signal‐to‐noise ratio, and noise amplification (g‐factors) as measured using the pseudo‐multiple replica method. Effects of smoothing, including contrast loss, are studied in synthetic phantom data. In the experiments presented, the contrast loss and spatial resolution are competitive with existing methods. Results for several brain images demonstrate significant improvements over GRAPPA at high acceleration factors in denoising performance with limited blurring or smoothing artifacts. In addition, the measured g‐factors suggest that DEnoising of Sparse Images from GRAPPA using the Nullspace method mitigates noise amplification better than both GRAPPA and L1 iterative self‐consistent parallel imaging reconstruction (the latter limited here by uniform undersampling). Magn Reson Med, 2012. © 2011 Wiley Periodicals, Inc.
Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam principles)
Authors: Kinsinger Christopher R. , Apffel James , Baker Mark , Bian Xiaopeng , Borchers Christoph H. , Bradshaw Ralph , Brusniak Mi‐Youn , Chan Daniel W. , Deutsch Eric W. , Domon Bruno , Gorman Jeff , Grimm Rudolf , Hancock William , Hermjakob Henning , Horn David , Hunter Christie , Kolar Patrik , Kraus Hans‐Joachim , Langen Hanno , Linding Rune , Moritz Robert L. , Omenn Gilbert S. , Orlando Ron , Pandey Akhilesh , Ping Peipei , Rahbar Amir , Rivers Robert , Seymour Sean L. , Simpson Richard J. , Slotta Douglas , Smith Richard D. , Stein Stephen E. , Tabb David L. , Tagle Danilo , Yates John R. , Rodriguez Henry 
Published: December 2011

AbstractPolicies supporting the rapid and open sharing of proteomic data are being implemented by the leading journals in the field. The proteomics community is taking steps to ensure that data are made publicly accessible and are of high quality, a challenging task that requires the development and deployment of methods for measuring and documenting data quality metrics. On September 18, 2010, the U.S. National Cancer Institute (NCI) convened the “International Workshop on Proteomic Data Quality Metrics” in Sydney, Australia, to identify and address issues facing the development and use of such methods for open access proteomics data. The stakeholders at the workshop enumerated the key principles underlying a framework for data quality assessment in mass spectrometry data that will meet the needs of the research community, journals, funding agencies, and data repositories. Attendees discussed and agreed up on two primary needs for the wide use of quality metrics: (i) an evolving list of comprehensive quality metrics and (ii) standards accompanied by software analytics. Attendees stressed the importance of increased education and training programs to promote reliable protocols in proteomics. This workshop report explores the historic precedents, key discussions, and necessary next steps to enhance the quality of open access data. By agreement, this article is published simultaneously in Proteomics, Proteomics Clinical Applications, Journal of Proteome Research, and Molecular and Cellular Proteomics, as a public service to the research community. The peer review process was a coordinated effort conducted by a panel of referees selected by the journals.
Probing Access Resistance of Solid‐State Nanopores with a Scanning‐Probe Microscope Tip
Authors: Hyun Changbae , Rollings Ryan , Li Jiali 
Published: December 2011

AbstractAn apparatus that integrates solid‐state nanopore ionic current measurement with a scanning‐probe microscope is developed. When a micrometer‐scale scanning‐probe tip is near a voltage‐biased nanometer‐scale pore (10–100 nm), the tip partially blocks the flow of ions to the pore and increases the pore access resistance. The apparatus records the current blockage caused by the probe tip and the location of the tip simultaneously. By measuring the current blockage map near a nanopore as a function of the tip position in 3D space in salt solution, the relative pore resistance increases due to the tip and ΔR/R0is estimated as a function of the tip location, nanopore geometry, and salt concentration. The amplitude of ΔR/R0also depends on the ratio of the pore length to its radius as Ohm's law predicts. When the tip is very close to the pore surface, ≈10 nm, experiments show that ΔR/R0depends on salt concentration as predicted by the Poisson and Nernst–Planck equations. Furthermore, the measurements show that ΔR/R0goes to zero when the tip is about five times the pore diameter away from the center of the pore entrance. The results in this work not only demonstrate a way to probe the access resistance of nanopores experimentally; they also provide a way to locate the nanopore in salt solution, and open the door to future nanopore experiments for detecting single biomolecules attached to a probe tip.