bluuebunny/crossref_metadata_2025_split huggingface dataset:
Alignment and statistical difference analysis of complex peptide data sets generated by multidimensional LC‐MS
Authors: America Antoine H. P. , Cordewener Jan H. G. , van Geffen Mark H. A. , Lommen Arien , Vissers Johannes P. C. , Bino Raoul J. , Hall Robert D. 
Published: December 2005

AbstractA method for high‐resolution proteomics analyses of complex protein mixtures is presented using multidimensional HPLC coupled to MS (MDLC‐MS). The method was applied to identify proteins that are differentially expressed during fruit ripening of tomato. Protein extracts from red and green tomato fruits were digested by trypsin. The resulting highly complex peptide mixtures were separated by strong cation exchange chromatography (SCX), and subsequently analyzed by RP nano‐LC coupled to quadrupole‐TOF MS. For detailed quantitative comparison, triplicate RP‐LC‐MS runs were performed for each SCX fraction. The resulting data sets were analyzed using MetAlign software for noise and data reduction, multiple alignment and statistical variance analysis. For each RP‐LC‐MS chromatogram, up to 7000 mass components were detected. Peak intensity data were compared by multivariate and statistical analysis. This revealed a clear separation between the green and red tomato samples, and a clear separation of the different SCX fractions. MS/MS spectra were collected using the data‐dependent acquisition mode from a selected set of differentially detected peptide masses, enabling the identification of proteins that were differentially expressed during ripening of tomato fruits. Our approach is a highly sensitive method to analyze proteins in complex mixtures without the need of isotope labeling.
DIGE compatible labelling of surface proteins on vital cells in vitro and in vivo
Authors: Mayrhofer Corina , Krieger Sigurd , Allmaier Günter , Kerjaschki Dontscho 
Published: December 2005

AbstractEfficient methods for profiling of the cell surface proteome are desirable to get a deeper insight in basic biological processes, to localise proteins and to uncover proteins differentially expressed in diseases. Here we present a strategy to target cell surface exposed proteins via fluorescence labelling using CyDye DIGE fluors. This method has been applied to human cell lines in vitro as well as to a complex biological system in vivo. It allows detection of fluorophore‐tagged cell surface proteins and visualisation of the accessible proteome within a single 2‐D gel, simplifying subsequent UV MALDI‐MS analysis.
Analysis of outer membrane proteome of Escherichia coli related to resistance to ampicillin and tetracycline
Authors: Xu Changxin , Lin Xiangmin , Ren Haixia , Zhang Yueling , Wang Sanying , Peng Xuanxian 
Published: December 2005

AbstractThe elucidation of the molecular details of antibiotic resistance will lead to improvements in extending the efficacy of current antimicrobials. In the current study, proteomic methodologies were applied to characterize functional outer membrane proteins (Omps) of E. coli K‐12 responded to tetracycline and ampicillin resistance for understanding of universal pathways that form barriers for antimicrobial agents. For this purpose, E. coli K‐12 expressional outer membrane proteome was characterized and identified with the use of 2‐DE and MALDI‐TOF/MS methods. Then, differential Omps due to tetracycline or ampcilin resistance were determined by comparison between tetracycline minimum inhibitory concentration (MIC)10, ampicillin MIC10, control0 and control10, showing 9 proteins with 11 spots for tetracycline and 8 protein with 9 spots for ampicillin, showing a difference in only 1 protein (decreased LamB in tetracyclin) between the two antibiotics. Among the proteins, 3 were known as antibiotic‐resistant proteins, including TolC, OmpC and YhiU, while FimD precursor, LamB, Tsx, YfiO, OmpW, NlpB were first reported here to be antibiotic‐resistance‐related proteins. Our findings will be helpful for further understanding of antibiotic‐resistant mechanism(s). This study also shows that the combination of Omp purification methods certainly contributes the sensitivity of Omp detection.
Proteome analysis of up‐regulated proteins in the rat spinal cord induced by transection injury
Authors: Ding Qinxue , Wu Zhe , Guo Yaojun , Zhao Congjian , Jia Yufeng , Kong Fanwen , Chen Bingyao , Wang Hongxia , Xiong Shaoxiang , Que Haiping , Jing Shuqian , Liu Shaojun 
Published: December 2005

AbstractThe inability of the CNS to regenerate in adult mammals propels us to reveal associated proteins involved in the injured CNS. In this paper, either thoracic laminectomy (as sham control) or thoracic spinal cord transection was performed on male adult rats. Five days after surgery, the whole spinal cord tissue was dissected and fractionated into water‐soluble (dissolved in Tris buffer) and water‐insoluble (dissolved in a solution containing chaotropes and surfactants) portions for 2‐DE. Protein identification was performed by MS and further confirmed by Western blot. As a result, over 30 protein spots in the injured spinal cord were shown to be up‐regulated no less than 1.5‐fold. These identified proteins possibly play various roles during the injury and repair process and may be functionally categorized as several different groups, such as stress‐responsive and metabolic changes, lipid and protein degeneration, neural survival and regeneration. In particular, over‐expression of 11‐zinc finger protein and glypican may be responsible for the inhibition of axonal growth and regeneration. Moreover, three unknown proteins with novel sequences were found to be up‐regulated by spinal cord injury. Further characterization of these molecules may help us come closer to understanding the mechanisms that underlie the inability of the adult CNS to regenerate.
Copolymerization of vinylidene difluoride with hexafluoropropene in supercritical carbon dioxide
Authors: Beginn Uwe , Najjar Reza , Ellmann Jürgen , Vinokur Rostislav , Martin Roland , Möller Martin 
Published: December 2005

AbstractVinylidene difluoride and hexafluoropropene are copolymerized in supercritical carbon dioxide at 280 bar and 50 °C by means of free radical copolymerization, initiated by diethyl peroxydicarbonate. The first stages of the reaction were monitored by turbidity measurements and the time/conversion curve was followed gravimetrically to measure the initial rates of polymerization. The obtained copolymers possessed bimodal molecular weight distributions, their average comonomer composition was well described by the Lewis‐Mayo equation with the copolymerization parameters rVDF = 4.8 and rHFP = 0. The glass transition and melting temperatures of the copolymers are similar to that of the materials resulting from aqueous emulsion polymerization. © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 44: 1299–1316, 2006
Mechanical properties of high‐density polyethylene and crosslinked high‐density polyethylene in crude oil and its components
Authors: Ritums J. E. , Mattozzi A. , Gedde U. W. , Hedenqvist M. S. , Bergman G. , Palmlöf M. 
Published: December 2005

AbstractThe tensile and stress‐relaxation properties of an uncrosslinked and a loosely silane‐crosslinked high‐density polyethylene exposed to organic “crude‐oil” penetrants were assessed. The measurements were performed on penetrant‐saturated samples, surrounded by the organic liquid throughout the experiment. The penetrant solubilities in the two polymers were similar and in accordance with predicted values based on the solubility parameter method. The stiffness and strength of the swollen samples were significantly less than those of the dry samples, indicating a plasticization of the amorphous component. Raman spectroscopy on polyethylene exposed to deuterated n‐hexane revealed a penetrant‐induced partial melting/dissolution of the crystal surface and an intact crystal core component. The stress‐relaxation rates, within the time frame of the experiment (∼1 s to 18 h), were approximately the same, independent of silane‐crosslinks and the presence of penetrants. This indicated that the mechanical α‐relaxation, which is the main relaxation process occurring in the measured time interval, was not affected by the penetrants. Consequently, its rate seemed to be independent of the crystal surface dissolution (decrease in the content of crystal‐core interface). The shape of the “log stress–log time” curves of the swollen samples was, however, different from that of the dry samples. This was most likely attributed to a time‐dependent saturation of penetrant to a higher level associated with the stretched state of the polymer sample. The silane crosslinks affected only the elongation at break, which was less than that of the uncrosslinked material. © 2005 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 44: 641–648, 2006
The Effect of Pressing Parameters on the Mechanical Properties of Plastic Bonded Explosives
Authors: Graff Thompson Darla , Olinger Bart , DeLuca Racci 
Published: December 2005

AbstractQuasi‐static, uniaxial mechanical properties were measured for a series of PBX 9501 parts that were compacted using a permutation of various pressing parameters. Results were analyzed in terms of specimen density as well as pressing parameters. These data led to a second set of tests where PBX 9501 parts were compacted using various dwell times and temperatures, all other pressing parameters being held constant. Quasi‐static tensile data for these parts indicated that for the given range of parameters and specimen densities, the compaction temperature has a larger effect on the mechanical properties than does the dwell time. Moreover, for the range of parameters used, higher compaction temperatures and lower dwell times gave the compacted part more strength and toughness. Desired mechanical characteristics may be achieved by the appropriate selection of pressing conditions.
New High‐Nitrogen Materials Based on Nitroguanyl‐Tetrazines: Explosive Properties, Thermal Decomposition and Combustion Studies
Authors: Chavez David E. , Tappan Bryce C. , Hiskey Michael A. , Son Steve F. , Harry Herbert , Montoya Dennis , Hagelberg Stephanie 
Published: December 2005

AbstractThis paper describes the explosive sensitivity and performance properties of two novel high‐nitrogen materials, 3,6‐bis‐nitroguanyl‐1,2,4,5‐tetrazine (1, (NQ2Tz)) and its corresponding bis‐triaminoguanidinium salt (2, (TAG)2(NQ)2Tz)). These materials exhibit very low pressure dependence in burning rate. Flash pyrolysis/FTIR spectroscopy was performed, and insight into this interesting burning behavior was obtained. Our studies indicate that 1 and 2 exhibit highly promising energetic materials properties.
Ignition Characteristics of Ti/Teflon Pyrolants: Safety Igniter with Partition
Authors: Kuwahara Takuo , Tohara Chiharu , Kohno Takehiro , Shibamoto Hidefumi 
Published: December 2005

AbstractBy using partitions in smoke generators, luminous flame agents or other pyrotechnic agents, the vapor and sublimated materials are confined in a chamber. Titanium (Ti), polytetrafluoroethylene (Teflon), and Viton pyrolants (TTV), which generate high temperature products, can be used in a partition type igniter. The ignition delay time, τig, decreased with the increase of the concentration of Ti, ξ(Ti), and also the physical ignition delay time, τp, decreased with the increase of ξ(Ti). On the other hand the chemical ignition delay time, τc, remained unchanged in the range of ξ(Ti) from 0.4 to 0.7. As τp of TTV pyrolants is larger than τc, the ignition delay time is dominated by physical processes.
The Poly‐Rho Test as a Screening Tool for Explosive Performance
Authors: Harry Herbert H. , Uher Kenneth J. , Hagelberg Stephanie I. , Hartline Ernest L. 
Published: December 2005

AbstractA screening test was developed at Los Alamos National Laboratory [1] that can be used to decide if a newly synthesized/formulated explosive might warrant further development. The test consists of firing a rate‐stick composed of 12.7 mm diameter by 12.7 mm high pellets of different densities ordered from lowest to highest, initiated by a detonator at the low‐density end of the stick. This poly‐rho test yields detonation velocities over a range of densities using only the small amount of the explosive typically generated by the synthetic organic chemist at an early stage of the scale‐up process. The amount of material required is far less than that required for the typical rate‐stick series. This paper presents results on poly‐rho tests that were conducted on three explosives commonly used at Los Alamos National Laboratory, namely PBX 9501, PBX 9502 and PETN. The results are compared with empirical detonation‐theory predictions and existing explosive experimental data, with good agreement in all cases.
Synthesis and Characterization of 4,4′,5,5′‐Tetranitro‐2,2′‐Bi‐1H‐imidazole (TNBI)
Authors: Cho Soo Gyeong , Cho Jin Rai , Goh Eun Mee , Kim Jae‐Kyung , Damavarapu Reddy , Surapaneni Rao 
Published: December 2005

AbstractWe synthesized 4,4′,5,5′‐tetranitro‐2,2′‐bi‐1H‐imidazole (TNBI), which may serve as a new energetic filler for high explosive formulations. TNBI was synthesized by treating an excess amount of sodium nitrate with 2,2′‐bi‐1H‐imidazole (BI), which was produced from glyoxal and ammonia gas. The overall synthetic yield was 32%. The synthesized TNBI was characterized by performing various chemical analyses including NMR, IR, and CHN analyses. Small scale sensitivity tests were carried out at both research institutes (ADD and ARDEC). The sensitivity results varied from ‘more sensitive than RDX’ to ‘substantially less sensitive than RDX’ according to the purity and conditions of the test samples. Based on our careful characterizations, this large variation in sensitivity was attributed to the moisture content that was present in the test samples due to a hygroscopic nature of TNBI. We also found that the hygroscopic nature of TNBI changed significantly due to the amount of impurities, especially sulfates.
Enhancement of intermittent androgen ablation by “off‐cycle” maintenance with finasteride in LNCaP prostate cancer xenograft model
Authors: Eggener Scott E. , Stern Jeff A. , Jain Pankaj M. , Oram Shane , Ai Junkui , Cai Xiaoyan , Roehl Kim A. , Wang Zhou 
Published: December 2005

AbstractBACKGROUNDIntermittent androgen ablation (IAA) was developed with the intention of delaying progression of prostate cancer to androgen‐independence and improving quality of life. Our previous studies suggest that relative to dihydrotestosterone (DHT), testosterone (T) is a weak inducer of proliferation and a more potent inducer of differentiation. We hypothesize that administration of finasteride (F), a type‐II 5‐α‐reductase inhibitor that increases T and decreases DHT, during the IAA “off‐cycle” would enhance the efficacy.METHODSAfter LNCaP tumor establishment, nude mice were castrated and randomized to continuous androgen ablation (CAA), continuous androgen ablation plus finasteride (CAA + F), intermittent androgen ablation (IAA), or intermittent androgen ablation plus finasteride (IAA + F).RESULTSAfter one cycle of therapy, mice treated with IAA + F had significantly less tumor growth than the other treatment groups (P = 0.002). Mice treated with IAA + F had the best survival (P = 0.048) and were 3–5 times more likely to be alive 70 days following treatment initiation.CONCLUSIONSIAA with finasteride provides the most favorable tumor growth kinetics and survival compared to both CAA and standard IAA. Prostate © 2005 Wiley‐Liss, Inc.
PAC1‐Rnullisoform expression in human prostate cancer tissue
Authors: Mammi Caterina , Frajese Giovanni V. , Vespasiani Giuseppe , Mariani Stefania , Gnessi Lucio , Farini Donatella , Fabbri Andrea , Frajese Gaetano , Moretti Costanzo 
Published: December 2005

AbstractBACKGROUNDPACAP is a member of the VIP/GHRH family of neuropeptides and has important effects on prostate cell proliferation. Here we analyze the expression and localization of PACAP and its specific receptor variants (PAC1‐R) in tissues collected from patients undergoing prostate biopsy and surgery for benign prostatic hyperplasia (BPH) and prostate cancer (PCa).METHODSReverse transcriptase (RT)‐polymerase chain reaction (PCR), DNA sequencing, and immunohistochemistry.RESULTSPACAP and PAC1‐R were localized by immunohistochemistry in the prostate tissue. While in healthy and BPH tissues PAC1‐R positive staining is present in all the epithelial cells lining the lumen of the acini and in some stromal cells (mostly in the apical portion of the cells), in PCa tissues, anti‐PAC1‐R antibody stained the apical portion of the cells. We provide evidence that PAC1‐Rnulland SV1/SV2variants are all present in normal and hyperplastic tissues, while in PCa tissue PAC1‐Rnullis the most relevant receptor variant expressed.CONCLUSIONSOur data demonstrates that the PAC1‐Rnullvariant is the most relevant isoform expressed in human PCa tissue being suggestively related with the events determining the outcome of prostate cancer. © 2005 Wiley‐Liss, Inc.
Murine androgen‐independent neuroendocrine carcinoma promotes metastasis of human prostate cancer cell line LNCaP
Authors: Uchida Kohsuke , Masumori Naoya , Takahashi Atsushi , Itoh Naoki , Kato Kazunori , Matusik Robert J. , Tsukamoto Taiji 
Published: December 2005

AbstractBACKGROUNDAlthough neuroendocrine (NE) cells in prostate cancer have been speculated to accelerate the growth and progression of surrounding cancer cells, the evidence is as yet inconclusive. We investigated the effect of an NE allograft (NE‐10) and its cell line, NE‐CS, which were established from the prostate of the LPB‐Tag 12T‐10 transgenic mouse, on human prostate cancer cell line LNCaP.METHODSThe proliferation and pulmonary metastasis of LNCaP xenografts in athymic mice with and without NE‐10 allografts were evaluated. Boyden chamber assay and microarray analysis were performed to investigate changes in invasion/migration and mRNA of LNCaP cells under the influence of the NE cells, respectively.RESULTSNE‐10 did not influence the proliferation of LNCaP. The pulmonary metastasis of LNCaP with NE‐10 significantly increased compared to mice without it. The NE‐CS cells accelerated the in vitro invasion/migration of adenocarcinoma cells. Increased expression of mRNA of gelsolin was observed in LNCaP cells incubated with the supernatant of NE‐CS cells.CONCLUSIONSThe NE‐10 allograft promotes pulmonary metastasis of subcutaneously inoculated LNCaP cells by facilitating cell invasion. Secretions from NE cells upregulate the expression of gelsolin, which is an actin‐binding protein, resulting in acceleration of the migration of LNCaP cells. © 2005 Wiley‐Liss, Inc.
Prostatic fluid concentrations of isoflavonoids in soy consumers are sufficient to inhibit growth of benign and malignant prostatic epithelial cells in vitro
Authors: Hedlund Tammy E. , Bokhoven Adrie van , Johannes Widya U. , Nordeen Steven K. , Ogden Lorraine G. 
Published: December 2005

AbstractBACKGROUNDThe differential intestinal metabolism of the soy isoflavones is likely to influence the ability of soy to prevent prostate cancer. While daidzein, genistein, and equol have direct antiproliferative effects on prostatic epithelial cells in vitro, there are no such data for the isoflavone glycitein, or seven metabolites: O‐desmethylangolensin (ODMA), 6‐hydroxyODMA (6H‐ODMA), dihydrodaidzein (DHD), cis‐4‐hydroxyequol (C4HE), 3′‐hydroxydaidzein (3HD), 6‐hydroxydaidzein (6HD), and 8‐hydroxydaidzein (8HD). In the current study, the in vitro activities of these compounds were elucidated, and the active ranges of concentrations were compared to that found in Caucasian prostatic fluid (PF) and plasma samples.METHODSThe effects of isoflavonoids on cell growth, cell cycle distribution, and apoptosis (active Caspase 3) were examined on benign prostatic epithelial cells (PrEC), and the prostate cancer cell line LNCaP.RESULTSPF concentrations of genistein, equol, and daidzein (but not ODMA or DHD) were often within the ranges that reduce PrEC growth in vitro. Profound differences in sensitivities were observed with LNCaP. The hydroxydaidzeins, C4HE, and 6H‐ODMA had significant inhibitory effects at 10−5M on PrEC growth (but not LNCaP). Glycitein had significant effects on both. Reductions in cell growth were typically associated with both changes in cell cycle distribution and Caspase 3 activation. When five isoflavonoids were used in combination at concentrations present in PF samples, synergistic effects were observed.CONCLUSIONThe profound differences in sensitivities of prostatic epithelial cells to these compounds along with their synergistic effects suggest that multiple metabolites in vivo may be optimal for preventing prostate cancer. Prostate © 2005 Wiley‐Liss, Inc.
Characterization of an antibody that can detect the Kai1/CD82 murine metastasis suppressor
Authors: Custer Mary C. , Risinger John I. , Hoover Shelley , Simpson R. Mark , Patterson Tricia , Barrett J. Carl 
Published: December 2005

AbstractBACKGROUNDKai1, also known as CD82, is a member of the tetraspanin family (TM4SF). The human homolog, KAI1, is an activation antigen of T‐cells and is a metastasis suppressor for prostate and other cancers. Little is known about the mouse protein because of the lack of antibody reagents.METHODSPeptide immunized rabbits were used to generate polyclonal antibody to Kai1. The antibody was analyzed using immunoblotting, flow cytometry, and immunohistochemistry.RESULTSThis antibody specifically recognizes murine Kai1 protein, crossreacts with rat Kai1 but not with human KAI1. The normal tissue distribution of this protein in mice is shown to be similar to that of the human homolog. Interestingly, mouse prostatic epithelium showed differential expression within the lobes.CONCLUSIONThis antibody, the first described that can specifically detect murine Kai1/CD82, should be very useful in addressing the mechanism of action of Kai1 in metastatic suppression. Prostate 66:567–577, 2006. © 2005 Wiley‐Liss, Inc.
A dynamic N‐capping motif in cytochrome b5: Evidence for a pH‐controlled conformational switch
Authors: Davis Ronald B. , Lecomte Juliette T.J. 
Published: December 2005

AbstractApocytochrome b5 is a marginally stable protein exhibiting under native conditions a slow conformational exchange in its C‐terminal region. The affected elements of secondary structure include a 310‐helix containing at its N‐terminus a histidine Ncap and a subsequent proline. Participation of the neutral histidine side‐chain in backbone amide capping lowers the imidazole pKa. To explore the nature of the conformational exchange in the protein and determine whether it is related to cis–trans isomerization of the His–Pro bond, three octapeptides encompassing the helix were synthesized and studied by NMR spectroscopy. One corresponded to the wild‐type sequence, the second was the D‐histidine epimer, and the third contained an alanine in place of the proline. It was found that the rates of cis–trans interconversion in the proline‐containing peptides were slower than the rates of the conformational exchange in the protein. In addition, the wild‐type peptide hinted at a predisposition for Ncap formation when in the trans configuration. Analysis of the pH response of the peptides and protein suggested that at pH near neutral, the conformational exchange detected in the protein involved only species with a trans His–Pro bond and could be approximated with a three‐state model by which the terminal helix sampled a locally unfolded state. This state, which contained an uncapped histidine with a normal pKa, partitioned into neutral and protonated populations according to pH. The intrinsic conformational bias of the wild‐type peptide and the pH‐driven equilibria illustrated how a 310‐element could serve as a nucleation site for structural rearrangement. Proteins 2006. © 2005 Wiley‐Liss, Inc.