bluuebunny/crossref_metadata_2025_split huggingface dataset:
In situSynthesis of Oligonucleotide and Detection of Gold‐label‐silver‐stain on PTFE Slices
Authors: Tan Mei‐Jun , Tang Jian‐Xin , Chen Hong 
Published: October 2005

Abstract Poly(tetrafluoroethylene) (PTFE) was treated with plasma in a mixture of nitrogen and hydrogen (1:2 in volume). X‐ray photoelectron spectroscopy (XPS) demonstrated the success of amino group grafting. The as‐treated PTFE slices were successively applied to the in situ synthesis of oligonucleotides. With the detection of gold‐label‐silver‐stain, the hybridization signals were recorded with a gel document and analysis system. A target DNA concentration as low as 10 pmol/L could be detected. The complementary and mismatched sequences were distinguished clearly, and the ratio of background‐subtracted gray scale values for perfect match:1 base mismatch:2 base mismatch:3 base mismatch was 72:44.4:22.5:11.4. The sensitivity of in situ synthesis system was 1 order of magnitude higher than that of spotting system, and the signal of the former was about 1.5 times stronger than that of the latter under the same target DNA concentration. These plasma modified PTFE slices might open novel prospects for the in situ synthesis of DNA micro‐arrays.
Facile Synthesis and Characterization of Bioactive N‐[(1‐Ferrocenylethylidene)amino]‐ N′ ‐β‐D‐glycopyranosylthiourea
Authors: Zhang Shu‐Sheng , Yang Bo , Li Hui‐Xiang , Jiao Kui 
Published: October 2005

AbstractSeveral novel N‐[(1‐ferrocenylethylidene)amino]‐N′ ‐β‐D‐glycopyranosylthioureas have been efficiently synthesized via a six‐step procedure, utilizing three monosaccharides (D‐glucose, D‐galactose and D‐xylose) as starting materials, respectively. They have been preliminarily determined to display biological activity against certain fungi. The target compounds have been unambiguously characterized by spectroscopic method and elemental analysis. An initially alternative synthetic route, which was seemingly reasonable, has been excluded due to its inefficiency.
Penta‐Coordinate Phosphorus Intermediates Analysis on Phospho‐related Proteins
Authors: Li Wu , Ma Yuan , Zhao Yu‐Fen 
Published: October 2005

Abstract In this paper, based on known crystal structures of square pyramid (SP) and trigonal bipyramid (TBP) penta coordinated phosphorus compounds containing amino acid side chains, such as amino, carboxyl, hydroxyl or thiol, a software for survey the P(5)‐structure of phosphorylated proteins was derived. By this software, it was found that 382 of 398 phosphorus related kinases (96%) from current PDB could go through the penta‐coordinated phosphorus transition state or intermediate.
Precision radiotherapy for hemangiopericytomas of the central nervous system
Authors: Combs Stephanie E. , Thilmann Christoph , Debus Jurgen , Schulz‐Ertner Daniela 
Published: October 2005

AbstractBACKGROUNDRadiotherapy (RT) plays a major role in the management of hemangiopericytomas (HAP). The present analysis evaluates the role of precision RT in the management of HAP of the central nervous system (CNS) and represents one of the largest series of HAP treated with RT that can be found in the literature.METHODSOf 37 consecutive patients with histologically confirmed HAP who were treated at the institution between 1984 and 2004, the majority, 25 tumors, was localized within the skull base (n = 25) and 4 tumors were localized at the spine. In 25 patients, high‐precision RT was delivered as fractionated stereotactic RT or intensity modulated RT. Median age at primary diagnosis was 40.5 years (range, 10–77 yrs). After primary diagnosis, surgical resection was performed in 23 patients. A median total dose of 54 Gy was delivered in a fractionation of 5 × 1.8–2 Gy per week. The median planning target volume was 58.2 mL (range, 10–412 mL). The median follow‐up time was 34 months (range, 3–166 mos).RESULTSRadiotherapy was well tolerated by all patients. Seventeen patients of this series remain alive. Overall survival rates at 5 and 10 years are 100% and 64%, respectively. Actuarial survival rates after RT were 85% and 69% at 3 and 5 years, respectively. Progression‐free survival after RT 80% and 61% at 3 and 5 years, respectively.CONCLUSIONHigh‐precision RT is an effective and safe treatment modality for patients with HAP of the CNS and the spine and achieves highly acceptable tumor control, while sparing normal tissue. Cancer 2005. © 2005 American Cancer Society.
Matrix metalloproteinases in carcinoma of unknown primary
Authors: Karavasilis Vasilis , Malamou‐Mitsi Vasiliki , Briasoulis Evangelos , Tsanou Elena , Kitsou Evangelia , Kalofonos Haralambos , Fountzilas George , Fotsis Theodore , Pavlidis Nicholas 
Published: October 2005

AbstractBACKGROUNDThe purpose was to study proteolysis‐related molecules, matrix metalloproteinase‐2 (MMP‐2) and MMP‐9 and tissue inhibitor of metalloproteinases‐1 (TIMP‐1), in carcinoma of unknown primary (CUP).METHODSParaffin‐embedded tumor material from 75 patients diagnosed with CUP was used. Tumor histologies were adenocarcinoma (77%), undifferentiated carcinoma (19%), and squamous cell carcinoma (4%) and patients were categorized into favorable (62%) and unfavorable (38%) subsets. The tissue expression of MMP‐2, MMP‐9, and TIMP‐1 was assessed by use of specific monoclonal antibodies and evaluated by means of a visual staining score. The expression of molecules studied was analyzed against clinicopathological data.RESULTSMMP‐2 was found expressed in 69% (strong expression in 49%), MMP‐9 in 49% (strong in 36%), and TIMP‐1 in 79% (strong in 44%) of studied cases. The expression of MMP‐2 correlated positively with MMP‐9. TIMP‐1 was significantly higher in unfavorable compared with favorable tumors and was associated with a shorter survival of patients (7.5 vs. 12 mos). No other associations were detected.CONCLUSIONSMMP‐2, MMP‐9, and TIMP‐1 are widely expressed in CUP, suggesting an essential role of proteolysis in these tumors. TIMP‐1 may be considered a possible marker of poor prognosis in CUP patients. Cancer 2005. © 2005 American Cancer Society.
Phase II study of carboxyamidotriazole in patients with advanced renal cell carcinoma refractory to immunotherapy
Authors: Dutcher Janice P. , Leon Larry , Manola Judith , Friedland David M. , Roth Bruce , Wilding George 
Published: October 2005

AbstractBACKGROUNDThe current study evaluated the response rate and 6‐month time to disease progression of the antiangiogenesis agent carboxyamidotriazole (CAI) in patients with metastatic renal cell carcinoma (RCC).METHODSFifty‐seven patients with histologically confirmed metastatic RCC that progressed after biologic therapy (interferon or interleukin‐2) were enrolled. Four patients were ineligible. CAI was administered orally as a 28‐day cycle. Response and time to disease progression were evaluated.RESULTSFifteen of 53 eligible patients received > 5 cycles, but 13 patients eventually discontinued treatment because of progressive disease. The majority of toxicities were Grade 1. However, Grade 3/4 toxicities did occur, the majority of which were gastrointestinal in nature. One of 47 patients evaluable achieved a partial response (1.9%) lasting 172 days. Six of 53 patients were alive and disease progression free at 6 months from the start of treatment (11.3%). The median overall survival was 12.5 months. The survival periods in the low‐risk, intermediate‐risk, and poor‐risk groups were 16.2 months, 20.9 months, and 5.8 months, respectively.CONCLUSIONSPatients in trials of second‐line therapy appear to have a better prognosis than previously considered, in part because they are eligible for another clinical trial. CAI was found to have little to no effect on the natural history of progressive RCC. Cancer 2005. © 2005 American Cancer Society.
VEGF as a predictive marker of rectal tumor response to preoperative radiotherapy
Authors: Zlobec Inti , Steele Russell , Compton Carolyn C. 
Published: October 2005

AbstractBACKGROUNDNeoadjuvant radiotherapy for rectal cancer may result in tumor downstaging or complete tumor regression leading to greater sphincter preservation. The identification of molecular predictive markers of tumor response to preoperative radiotherapy would provide an additional tool for selecting patients most likely to benefit from treatment. The aim of this study was to determine whether VEGF expression in preirradiation tumor biopsies is a useful predictive marker of tumor response in patients with rectal cancer undergoing preoperative radiotherapy.METHODSImmunohistochemistry for VEGF was performed on 59 preirradiation biopsies from patients with completely responsive (ypT0) or nonresponsive tumors after preoperative radiotherapy. VEGF positivity was evaluated using several scoring methods and the association between VEGF and tumor response was compared. The distribution of VEGF scores was obtained as well as the mean VEGF expression in the two response groups.RESULTSThe mean VEGF expression in nonresponsive tumors (NR) was significantly greater than in completely responsive tumors (CR) (P = 0.0035). Nearly half (47%) of all CR tumors had a VEGF expression of 10% or less. Eleven tumors were negative (0% immunoreactivity) for the protein and all of these (100%) were complete responders. Fifty‐two percent of the NR tumors had VEGF scores of 80% or greater. The four scoring methods used to determine the association between VEGF and tumor response each produced significant results (P < 0.05).CONCLUSIONSThe results of this study indicate that VEGF assessed immunohistochemically from preirradiation tumor biopsies may be a useful marker of rectal tumor response to preoperative radiotherapy. Cancer 2005. © 2005 American Cancer Society.
Crystal Structures, EPR Spectra, and Magnetic Properties of a Series of Ionic Multi‐Component Complexes [(TBPDA)2·(C60·–)·(D+)] (D = Cp*2Cr, Cp*2Co, TDAE)
Authors: Konarev Dmitri V. , Kovalevsky Andrey Yu. , Khasanov Salavat S. , Saito Gunzi , Otsuka Akihiro , Lyubovskaya Rimma N. 
Published: October 2005

AbstractNew ionic multi‐component complexes [(TBPDA)2·(C60·–)·(D+)] [TBPDA = N,N,N′,N′‐tetrabenzyl‐p‐phenylenediamine; D = decamethylchromocene (Cp*2Cr, 1) and decamethylcobaltocene (Cp*2Co, 2)] were obtained additionally to previously characterized [(TBPDA)2·(C60·–)·(TDAE·+)] [TDAE = tetrakis(dimethylamino)ethylene, 3]. The presence of D+, C60·–, and neutral TBPDA in 1–3 was proved by the IR and UV/Visible/NIR spectra. D+ and C60·– form loose layers in 1 and 3 and are spatially separated by bulky TBPDA molecules. The C60·– radical anions alternate in the layer with the phenylene groups of TBPDA to form π‐π stacking, whereas disordered Cp*2Cr+ cations are isolated in the voids formed by eight benzyl groups of TBPDA. The EPR spectra of the complexes show single Lorentzian lines with g = 2.2526 and ΔH = 215 mT (1), g = 1.9999 and ΔH = 6.7 mT (2), and g = 2.0009 and ΔH = 2.93 mT (3) at room temperature. The EPR signal of 2 was attributed to C60·– (Cp*2Co+ is diamagnetic) and those in 1 and 3 to resonating signals between C60·– (g = 1.9996–2.0000) and Cp*2Cr+ [an asymmetric EPR signal with g[perp] = 4.02(1) and g[par] = 2.001(1)] (1) or TDAE·+ (g = 2.0035; 3) due to indirect coupling. The EPR signals from 2 and 3 are split into two components below 50 and 60 K, respectively, which shift in the opposite directions (to lower and higher fields) with decreasing temperature. The magnetic moments of 1–3 decrease below 50–100 K. Both effects are associated with the formation of field‐induced short‐range antiferromagnetically ordered clusters. It is shown that the D+ cations do not noticeably affect this interaction. Most probably, it is realized mainly between C60·– spins within the layer and is mediated by the phenylene groups of TBPDA. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2005)
Kinetic Inertness and Electrochemical Behavior of Copper(II) Tetraazamacrocyclic Complexes: Possible Implications for in Vivo Stability
Authors: Woodin Katrina S. , Heroux Katie J. , Boswell C. Andrew , Wong Edward H. , Weisman Gary R. , Niu Weijun , Tomellini Sterling A. , Anderson Carolyn J. , Zakharov Lev N. , Rheingold Arnold L. 
Published: October 2005

AbstractThe kinetic inertness of copper(II) complexes of several carboxymethyl‐armed cyclams and cyclens in 5 M HCl have been determined confirming that the complex derived from cross‐bridged cyclam (Cu‐CB‐TE2A) is by far the most resistant to acid decomplexation. FT‐IR studies in D2O solution revealed its unique resistance to full carboxylate protonation and its retention of coordination by both pendant arms even in 1 M DCl. The X‐ray structure of its monoprotonated form, [Cu‐CB‐TE2AH]+, also established full coordination by both COO– and COOH pendant arms in the solid state. Cyclic voltammograms of four carboxymethyl pendant‐armed cyclam and cyclen complexes in aqueous solution were obtained with only Cu‐CB‐TE2A displaying a quasi‐reversible CuII/CuI reduction wave. These indicators correlate with the superior in vivo behavior of this complex and its bifunctional conjugate. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2005)
Interaction Between Terminal Zinc–Porphyrins in a U‐Shaped Trimeric Porphyrin Array Bearing Chiral Amino Acid Tails
Authors: Arai Toru , Takei Kiyoshi , Ogawa Yoshifumi , Nishino Norikazu 
Published: October 2005

AbstractA U‐shaped trimeric porphyrin array with a zinc/free‐base/zinc arrangement (5ZFZ) and its derivatives were synthesized in order to investigate the interacting porphyrins in organic solvents. The porphyrin array is comprised of an αα‐atropisomeric bis(ortho‐aminophenyl)porphyrin free‐base as the template, a pair of zinc–porphyrins at the termini, achiral glycine spacers linking the porphyrins, and chiral L‐leucine derivatives attached to the template in the opposite direction of the zinc–porphyrins. 1H NMR (high‐field shifts of some pyrrole signals), UV/Vis (split Soret band), and CD spectra (exciton‐coupled Cotton effect) show the close assembly of the terminal zinc–porphyrins of 5ZFZ in CDCl3 and CH2Cl2. In contrast, the characteristic spectra for the interacting porphyrins do not appear for the trimeric array with three free‐base porphyrins (5F3) and the dimeric array with a zinc/free‐base arrangement (9ZF). (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2005)
Antimalarial Polyketide Cycloperoxides from the Marine SpongePlakortis simplex
Authors: Campagnuolo Claudio , Fattorusso Ernesto , Romano Adriana , Taglialatela‐Scafati Orazio , Basilico Nicoletta , Parapini Silvia , Taramelli Donatella 
Published: October 2005

AbstractThree new (5–7) and two known (4 and 8) polyketide derivatives have been isolated from the Caribbean sponge Plakortis simplex. Their stereostructures have been determined by spectroscopic methods and chemical transformations that include Zn‐mediated reduction and Dess–Martin oxidation, and by application of Mosher’s method. The cycloperoxide derivatives plakortide Q (7) and compound 8 were evaluated for their in vitro antimalarial activity against chloroquine‐sensitive and chloroquine‐resistant strains of Plasmodium falciparum. The lower potency of these molecules relative to plakortin indicates that the change of configuration at C‐3 exerts negative effects on the antimalarial activity. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2005)
Ti‐Mediated Synthesis of Aminocyclopropyl‐Substituted Carbohydrates
Authors: Laroche Christophe , Behr Jean‐Bernard , Szymoniak Jan , Bertus Philippe , Plantier‐Royon Richard 
Published: October 2005

AbstractCarbohydrates bearing aminocyclopropyl moieties were conveniently prepared from the corresponding nitriles by titanium‐mediated addition of Grignard reagents. A wide range of protective groups are tolerated. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2005)
Spirangien A and B, Highly Cytotoxic and Antifungal Spiroketals from the Myxobacterium Sorangium cellulosum: Isolation, Structure Elucidation and Chemical Modifications
Authors: Niggemann Jutta , Bedorf Norbert , Flörke Ulrich , Steinmetz Heinrich , Gerth Klaus , Reichenbach Hans , Höfle Gerhard 
Published: October 2005

AbstractTwo novel highly cytotoxic metabolites, spirangien A (1) and B (2), were isolated from the myxobacterium Sorangium cellulosum (strain So ce90). The structures were elucidated by detailed NMR spectroscopic analysis. The previously unknown molecular framework common to spirangien A and B includes a highly functionalized spiroketal core structure, a side chain bearing a pentaene chromophore and a terminal carboxyl group, and a total of thirteen stereocenters. The absolute configuration at C‐3 was determined by degradation and subsequent fragment analysis by GC. The relative stereochemistry of the spiroketal structure was proposed on the basis of vicinal proton couplings and ROESY data for hydroperoxide derivative 4, obtained by ozonolysis of spirangien A, and for 1,3‐diene 5, obtained by cross‐metathesis with ethylene. X‐ray crystal structure analysis of 5 confirmed its structure and unambiguously provided the complete relative stereochemistry of all twelve stereocenters. The 1,3‐diene derivative 5 still shows strong cytotoxic activity. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2005)
Facile Access to Isotopically Labelled Valylleucyl Anilides as Biomarkers for the Quantification of Hemoglobin Adducts to Toxic Electrophiles
Authors: Belov Vladimir N. , Müller Michael , Ignatenko Oleg , Hallier Ernst , de Meijere Armin 
Published: October 2005

AbstractAn easy and efficient synthesis of valylleucyl anilide (HValLeuNHPh) and labelled HVal(13C5,15N)LeuNHPh has been developed. Derivatization of these substances with oxirane, acrylonitrile, epichlorohydrin, glyceraldehyde and other aldehydes gives a series of reference substances and internal standards for the quantitative evaluation of human exposure to toxic electrophiles by quantitative determination of their hemoglobin adducts. Coupling of N‐Z‐N‐Me‐Val(13C5,15N)OH with HLeuNHPh followed by hydrogenolysis affords N–Me–Val(13C5,15N)LeuNHPh for quantification of the exposure to methylating agents. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2005)
Efficient Synthesis of 1,2,3‐Triazole‐Fused Bicyclic Compounds from Aldoses
Authors: Dolhem Franck , Al Tahli Fathia , Lièvre Catherine , Demailly Gilles 
Published: October 2005

AbstractWe would like to report an expedient synthesis of 1,2,3‐triazole‐fused bicyclic compounds starting from naturally occurring carbohydrates. These imino sugars were prepared in four steps from glyco‐ynitols, readily available from monosaccharides. The title compounds were prepared by intramolecular 1,3‐dipolar cycloaddition of azidoalkynes in a one‐pot substitution/thermal cyclization procedure. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2005)
Reaction kinetics for the degradation of phenol and chlorinated phenols using Fenton's reagent
Authors: De Asim K. , Dutta Binay K. , Bhattacharjee Sekhar 
Published: October 2005

AbstractFenton's reaction is an advanced treatment technology often used for the removal of hazardous and refractory organic compounds from industrial wastewaters. It can effectively be used to degrade phenol and chlorophenols. The initial contaminant concentrations as well as the concentration of hydrogen peroxide and ferrous ions in aqueous solution have a significant effect on the effective degradation of contaminants. For a particular concentration of initial substrate in solution there should be an optimum level of ferrous ion concentration in the reaction medium.Based on experimental observations, a probable mechanism for Fenton's degradation kinetics has been proposed and a rate equation developed. From the rate expression, OH· radical reaction rate constants for the degradation of three compounds—phenol and o‐ and p‐chlorophenols—in Fenton reaction were calculated to have values of 2.53 × 107, 2.38 × 107, and 2.45 × 107 m3 mol−1 s−1, respectively. © 2005 American Institute of Chemical Engineers Environ Prog, 2005
Drug entrapment in silica microspheres through a single step sol–gel process and in vitro release behavior
Authors: Yilmaz Elvan , Bengisu Murat 
Published: October 2005

AbstractA single step sol–gel process was used to precipitate silica microspheres containing ibuprofen or naproxen for controlled drug delivery applications. The drug release behavior from these systems was analyzed in vitro. Pure ibuprofen and naproxen exhibited linear release with time, while sol–gel silica entrapped drugs were released with a logarithmic time dependence starting with an initial burst effect followed by a gradual decrease. Microscopic analysis combined with gravimety and infrared spectroscopy indicated that some of the drug is entrapped as large crystals attached to silica microspheres while the rest is encapsulated inside the microspheres. Drug‐loaded silica microspheres with no open porosity and with a narrow particle size distribution were obtained. Both erosion of the microspheres and diffusion through them contributed to drug release. Sol–gel precipitation of silica microspheres is a promising method for drug entrapment and controlled release. © 2005 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 2006
Scalable molecular dynamics with NAMD
Authors: Phillips James C. , Braun Rosemary , Wang Wei , Gumbart James , Tajkhorshid Emad , Villa Elizabeth , Chipot Christophe , Skeel Robert D. , Kalé Laxmikant , Schulten Klaus 
Published: October 2005

AbstractNAMD is a parallel molecular dynamics code designed for high‐performance simulation of large biomolecular systems. NAMD scales to hundreds of processors on high‐end parallel platforms, as well as tens of processors on low‐cost commodity clusters, and also runs on individual desktop and laptop computers. NAMD works with AMBER and CHARMM potential functions, parameters, and file formats. This article, directed to novices as well as experts, first introduces concepts and methods used in the NAMD program, describing the classical molecular dynamics force field, equations of motion, and integration methods along with the efficient electrostatics evaluation algorithms employed and temperature and pressure controls used. Features for steering the simulation across barriers and for calculating both alchemical and conformational free energy differences are presented. The motivations for and a roadmap to the internal design of NAMD, implemented in C++ and based on Charm++ parallel objects, are outlined. The factors affecting the serial and parallel performance of a simulation are discussed. Finally, typical NAMD use is illustrated with representative applications to a small, a medium, and a large biomolecular system, highlighting particular features of NAMD, for example, the Tcl scripting language. The article also provides a list of the key features of NAMD and discusses the benefits of combining NAMD with the molecular graphics/sequence analysis software VMD and the grid computing/collaboratory software BioCoRE. NAMD is distributed free of charge with source code atwww.ks.uiuc.edu. © 2005 Wiley Periodicals, Inc. J Comput Chem 26: 1781–1802, 2005