bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analytical methods for multiresidue determination of sulfonamides and trimethoprim in meat and ground water samples by CE‐MS and CE‐MS/MS
Authors: Soto‐Chinchilla Jorge J. , García‐Campaña Ana M. , Gámiz‐Gracia Laura 
Published: October 2007

AbstractThis paper presents two methods based on CZE‐MS detection and CZE‐MS/MS detection developed for the multiresidue determination of ten sulfonamides (sulfapyridine, sulfadoxin, sulfamethazine, sulfadimethoxine, sulfameter, sulfamerazine, sulfachlorpyridazine, sulfadiazine, sulfamethoxazole, and sulfamethizole) and a potentiator, trimethoprim (TMP), whose contents are regulated by the EU Council Regulation no. 2377/90 in animal edible tissues. Experimental designs were employed to optimize the electrospray conditions. MS/MS experiments using an IT as analyzer operating in multiple reaction monitoring (MRM) mode were carried out to achieve the minimum number of points according to the 2002/657/EC European Decision for unambiguous identification. The proposed procedures have been compared in terms of the performance characteristics and trueness. The limits of detection and quantification were in all cases lower than the maximum residue limits legislated for these compounds and the recoveries were satisfactory, being possible the application for their monitoring in foodstuff of animal origin and in environmental samples, allowing the determination of sulfonamides and TMP residues in meat and in superficial water in the low μg/L range.
Functional assays in high‐resolution clear native gels to quantify mitochondrial complexes in human biopsies and cell lines
Authors: Wittig Ilka , Carrozzo Rosalba , Santorelli Filippo M. , Schägger Hermann 
Published: October 2007

AbstractWe introduce high resolution clear native electrophoresis (CNE) as a powerful technique to resolve enzymatically active mitochondrial complexes from cultured human cell lines and skeletal muscle biopsy samples. Quantitative enzymatic assays can be performed using small amounts of cultured cells with low mitochondria content, for example, around 10 mg of sedimented osteosarcoma cells (wet weight) which is equivalent to around 10 million cells. High resolution CNE offers general advantages for in‐gel catalytic activity assays compared to blue native electrophoresis. It seems especially suited for assaying mitochondrial ATP synthase and respiratory chain complexes I and II in cell models of human mitochondrial disorders and for detailed analyses of patient cells and tissues with defects in oxidative phosphorylation.
Interactions between intakes of alcohol and postmenopausal hormones on risk of breast cancer
Authors: Nielsen Naja Rod , Grønbæk Morten 
Published: October 2007

AbstractAlcohol and postmenopausal hormone use are well‐established modifiable risk factors for breast cancer. Alcohol may decrease the metabolic clearance of estradiol, whereby the risk of breast cancer associated with hormone use may depend on blood alcohol levels. The objective is to determine whether alcohol interacts with hormone use on risk of breast cancer. The 5,035 postmenopausal women who participated in the Copenhagen City Heart Study were asked about their alcohol intake and hormone use at baseline in 1981–1983 and were followed until 2002 in the Danish cancer registry, with <0.1% loss to follow‐up. Proportional hazard models were used to analyze data. During follow‐up, 267 women developed breast cancer. Alcohol consumption was associated with a small increased risk of breast cancer (hazard ratio = 1.11 per drink/day, 95% CI: 0.99–1.25). Women who used hormones also had a higher risk of breast cancer (HR = 2.00, 95% CI: 1.52–2.61) compared to nonhormone users. We found an interaction between these 2 factors; those who had an intake of more than 2 drinks per day and took hormones had a risk of 4.74 (95% CI: 2.61–8.59) for breast cancer compared to abstainers who did not use hormones. Alcohol was not associated with breast cancer among women who did not use hormones (HR = 0.98 per drink/day, 95% CI: 0.82–1.78). In conclusion, the interaction between alcohol and hormone use should, if confirmed in other studies, have an impact both on the prescription of hormones and on sensible drinking limits for postmenopausal women. © 2007 Wiley‐Liss, Inc.
Toward robust QSPR models: Synergistic utilization of robust regression and variable elimination
Authors: Grohmann Rainer , Schindler Torsten 
Published: October 2007

AbstractWidely used regression approaches in modeling quantitative structure–property relationships, such as PLS regression, are highly susceptible to outlying observations that will impair the prognostic value of a model. Our aim is to compile homogeneous datasets as the basis for regression modeling by removing outlying compounds and applying variable selection. We investigate different approaches to create robust, outlier‐resistant regression models in the field of prediction of drug molecules' permeability. The objective is to join the strength of outlier detection and variable elimination increasing the predictive power of prognostic regression models. In conclusion, outlier detection is employed to identify multiple, homogeneous data subsets for regression modeling. © 2007 Wiley Periodicals, Inc. J Comput Chem 2008
Evaluation of the intramolecular basis set superposition error in the calculations of larger molecules: [n]helicenes and Phe‐Gly‐Phe tripeptide
Authors: Valdés Haydée , Klusák Vojtěch , Pitoňák Michal , Exner Otto , Starý Ivo , Hobza Pavel , Rulíšek Lubomír 
Published: October 2007

AbstractCorrelated ab initio calculations on large systems, such as the popular MP2 (or RI‐MP2) method, suffer from the intramolecular basis set superposition error (BSSE). This error is typically manifested in molecules with folded structures, characterized by intramolecular dispersion interactions. It can dramatically affect the energy differences between various conformers as well as intramolecular stabilities, and it can even impair the accuracy of the predictions of the equilibrium molecular structures. In this study, we will present two extreme cases of intramolecular BSSE, the internal stability of [n]helicene molecules and the relative energies of various conformers of phenylalanyl‐glycyl‐phenylalanine tripeptide (Phe‐Gly‐Phe), and compare the calculated data with benchmark values (experimental or high‐level theoretical data). As a practical and cheap solution to the accurate treatment of the systems with large anticipated value of intramolecular BSSE, the recently developed density functional method augmented with an empirical dispersion term (DFT‐D) is proposed and shown to provide very good results in both of the above described representative cases. © 2007 Wiley Periodicals, Inc. J Comput Chem 2008
DFT modeling of reactivity in an ionic liquid: How many ion pairs?
Authors: Bessac Fabienne , Maseras Feliu 
Published: October 2007

AbstractThe modeling of reactivity in an ionic liquid is examined with DFT and DFT/MM calculations on the SN2 intramolecular rearrangement of the Z‐phenylhydrazone of 3‐benzoyl‐5‐phenyl‐1,2,4‐oxadiazole into 4‐benzoylamino‐2,5‐diphenyl‐1,2,3‐triazole induced by amines. Experimental research has shown that the reaction occurs in 1‐butyl‐3‐methylimidazolium tetrafluoroborate, and in conventional organic solvents such as acetonitrile with comparable rates. The structure for the reactants, transition states and products for the rate‐determining step are optimized, and the energy barrier is computed in three different environments: gas phase, water solvent, and ionic liquid. The results are encouraging in describing the energy barrier in the ionic liquid. A simple model is formulated to explain the effect of the solvent in this particular process, and a procedure to study theoretically the reactivity in an ionic liquid is proposed. © 2007 Wiley Periodicals, Inc. J Comput Chem 2008
Revisiting the relationship between the bond length alternation and the first hyperpolarizability with range‐separated hybrid functionals
Authors: Jacquemin Denis , Perpéte Eric A. , Ciofini Ilaria , Adamo Carlo 
Published: October 2007

AbstractWe monitor the influence of the bond length alternation (BLA) modification on the static electronic polarizability and first hyperpolarizability of two polymethineimine oligomers. Four theoretical approaches are compared: HF, PBE0, LC‐ωPBE, and MP2. For the dodecamer, both HF and PBE0 are unable to foresee even the qualitative evolution of the first hyperpolarizability when varying the BLA. On the contrary, LC‐ωPBE provides (non)linear optics properties in agreement with MP2 results, especially for the longer chains. This confirms the interest of range‐separated hybrids for the computation of the (hyper)polarizabilities of extended π‐conjugated compounds. © 2007 Wiley Periodicals, Inc. J Comput Chem 2008
RNA conformational sampling. I. Single‐nucleotide loop closure
Authors: Mak C. H. 
Published: October 2007

AbstractWe consider the loop‐closure problem for nucleic acids and describe an efficient numerical algorithm for closing single‐nucleotide loops in nucleic acids. Using six new internal coordinates to represent the nucleotide conformation, which we call the R‐representation, the original closure problem with six free torsion angles in each nucleotide can be reduced to one with only four degrees of freedom. Simple numerical techniques have been used to solve the resulting loop‐closure equations, and a test of the closure algorithm on a set of RNAs consisting of more than 7000 nucleotides was able to regenerate the native torsion angles in every nucleotide in the test set without exception. We show how the conformational probability density transforms when the original torsion angle representation is mapped onto the new R‐representation. We also present statistical evidence showing that the δ and ν2 torsion angles are coupled, and how this coupling affects the conformation probability density in the R‐representation. In addition to the backbone, the same loop‐closure algorithm can also be applied to close the ribose ring. The algorithm is freely available at http://tyrosine.use.edu/closure. © 2007 Wiley Periodicals, Inc. J Comput Chem 2008
Can TD‐DFT calculations accurately describe the excited states behavior of stacked nucleobases? The cytosine dimer as a test case
Authors: Santoro Fabrizio , Barone Vincenzo , Improta Roberto 
Published: October 2007

AbstractBy using calculations rooted in the time dependent density functional theory (TD‐DFT) we have investigated how the lowest energy excited states of a face‐to‐face π‐stacked cytosine dimer vary with the intermonomer distance (R). The perfomances of different density functionals have been compared, focussing mainly on the lowest energy single excited state of the dimer (S1)2. TD‐PBE0, TD‐LC‐ωPBE, and TD‐M05‐2X provide a picture very similar to that obtained at the CASPT2 level by Merchan et al. (J Chem Phys 2006, 125, 231102), predicting that (S1)2 has a minimum for R ∼ 3 Å, with a binding energy of ∼0.5 eV, whereas TD‐B3LYP, TD‐CAM‐B3LYP, and TD‐PBE understimate the binding energy. However, independently of the functional employed, no low‐energy spurious charge transfer transitions are predicted by TD‐DFT calculations, also when a nonsymmetric dimer is investigated, providing encouraging indications for the use of TD‐DFT for studying the excited state of π‐stacked nucleobases. © 2007 Wiley Periodicals, Inc. J Comput Chem 2008
Application of response surface methodology to optimize the operation process for regeneration of acid and base using bipolar membrane electrodialysis
Authors: Zhang Xiaoyan , Lu Wenhua , Yang Pengbo , Cong Wei 
Published: October 2007

AbstractBACKGROUND: Bipolar membrane electrodialysis (BMED) has been widely used for desalination, concentration, separation, and purification in many fields. The purpose of this study is to optimize the operation conditions using response surface methodology (RSM) for the regeneration of sulfuric acid and ammonia from ammonium sulfate solution by BMED coupled with ammonia in situ stripping.RESULTS: A three‐factor central composite design of RSM was used to analyze the effect of operation conditions (current density, flow rate, initial acid concentration) on average current efficiency (ACE) and establish the optimal operation conditions. The ACE was 76.7 ± 2.2% under optimal operation conditions (current density 23.8 mA cm−2, flow rate 27.3 L h−1, initial acid concentration 0.09 mol L−1).CONCLUSION: A suitable regression model for predicting ACE within the ranges of variables used was developed based on experimental results. The operation conditions were optimized by RSM and the ACE obtained under the optimal operation conditions was in good agreement with the value predicted by the regression model (78%), which proved the validity of the model. Copyright © 2007 Society of Chemical Industry
Effects of tumor necrosis factor‐α on cell proliferation, prostaglandins and matrix‐metalloproteinases production in rat endometrial stromal cells cultured in vitro
Authors: Gamo Toru , Yamauchi Nobuhiko , Nishimura Kyohei , Watanabe Ryo , Matsumoto Kenji , Oozono Shinji , Kubota Kaiyu , He Pei‐Jian , Soh Tomoki , Hattori Masa‐aki 
Published: October 2007

AbstractTumor necrosis factor‐α (TNF‐α) is known as a pluripotent cell mediator, and it is implicated in the control of uterine cell growth, differentiation and function during estrous cycle and pregnancy. In this study, we investigated the effect of TNF‐α on endometrial stromal cells derived from rat uterus (rat endometrial stromal cells, RES). RES were isolated from rat endometrium at day 5 of pregnancy. Proliferation activities of RES were measured by using bromodeoxyuridine (BrdU) labeling kit, the productions of prostaglandin E2 (PGE2) and prostaglandin F2α (PGF2α) were measured by enzyme immunoassay kits and the production of matrix metalloproteinases (MMPs) was analyzed by gelatin‐zymography. TNF‐α, as well as epidermal growth factor and fibroblast growth factor‐2, significantly increased the proliferation activity of RES (P<0.05). TNF‐α selectively stimulated the production of PGE2 in RES (P<0.05), but not the production of PGF2α. Additionally, TNF‐α did not stimulate the production of MMPs in RES at the concentration of 5 ng/mL, compared with the control groups (P>0.05). In conclusion, this study demonstrates several regulational functions of TNF‐α on RES using in vitro culture system. The effects of TNF‐α on proliferation and MMP production of RES have been shown for the first time. We believe that these results demonstrate part of the functions of TNF‐α in endometrium and contribute to the better understanding of endometrial functions. J. Exp. Zool. 307A:699–707, 2007. © 2007 Wiley‐Liss, Inc.
An efficient RNA‐cleaving DNA enzyme can specifically target the 5′‐untranslated region of severe acute respiratory syndrome associated coronavirus (SARS‐CoV)
Authors: Wu Shuwen , Xu Junqiang , Liu Jiangxia , Yan Xuan , Zhu Xiaodong , Xiao Gengfu , Sun Lunquan , Tien Po 
Published: October 2007

AbstractBackgroundThe worldwide epidemic of severe acute respiratory syndrome (SARS) in 2003 was caused by a novel coronavirus called SARS‐CoV. We report the use of DNAzyme (catalytic DNA) to target the 5′‐untranslated region (5′UTR) of a highly conserved fragment in the SARS genome as an approach to suppression of SARS‐CoV replication. A mono‐DNA enzyme (Dz‐104) possessing the 10–23 catalytic motif was synthesized and tested both in vitro and in cell culture.Materials and methodsSARS‐CoV total RNA was isolated, extracted from the SARS‐CoV‐WHU strain and converted into cDNA. We designed a RNA‐cleaving 10–23 DNAzyme targeting at the loop region of the 5′UTR of SARS‐CoV. The designed DNAzyme, Dz‐104, and its mutant version, Dz‐104 (mut), as a control consist of 9 + 9 arm sequences with a 10–23 catalytic core. In vitro cleavage was performed using an in vitro transcribed 5′UTR RNA substrate. A vector containing a fused 5′UTR and enhanced green fluorescent protein (eGFP) was co‐transfected with the DNAzyme into E6 cells and the cells expressing eGFP were visualized with fluorescence microscopy and analyzed by fluorescence‐activated cell sorting (FACS).Results and conclusionsOur results demonstrated that this DNAzyme could efficiently cleave the SARS‐CoV RNA substrate in vitro and inhibit the expression of the SARS‐CoV 5′UTR‐eGFP fusion RNA in mammalian cells. This work presents a model system to rapidly screen effective DNAzymes targeting SARS and provides a basis for potential therapeutic use of DNA enzymes to combat the SARS infection. Copyright © 2007 John Wiley & Sons, Ltd.
AdΔ24 and the p53‐expressing variant AdΔ24‐p53 achieve potent anti‐tumor activity in glioma when combined with radiotherapy
Authors: Idema Sander , Lamfers Martine L.M. , van Beusechem Victor W. , Noske David P. , Heukelom Stan , Moeniralm Sharif , Gerritsen Winald R. , Vandertop W. Peter , Dirven Clemens M.F. 
Published: October 2007

AbstractBackgroundThe conditionally replicating adenovirus (CRAd) AdΔ24‐p53 replicates selectively in Rb mutant cells, and encodes the p53 suppressor protein. It has shown improved oncolytic potency compared to the parental control AdΔ24. As exogenous p53 has been shown to enhance radiosensitivity, the combination of AdΔ24‐p53 and AdΔ24 with radiotherapy was assessed in vitro and in vivo against the therapy resistant gliomas.MethodsIn glioma cells, multicellular spheroids and animal xenografts the efficacy of combination therapy was assessed. P53 phosphorylation, induction of apoptosis and viral replication were determined following single or combination therapies.ResultsIn vitro, AdΔ24‐p53 was more effective against glioma cells than the control AdΔ24. Addition of irradiation equally increased the efficacy of both AdΔ24‐p53 and AdΔ24 resulting in improved oncolysis compared to single agent treatment. Radiotherapy did not significantly change the replication kinetics of AdΔ24‐p53 or AdΔ24. No detectable increase in p53 phosphorylation was observed but combination of radiotherapy and AdΔ24‐p53 caused an increase in the percentage of apoptotic cells. In vivo, combination therapy with either AdΔ24 or AdΔ24‐p53 significantly increased the number of mice demonstrating tumor regression (100%) as well as long‐term survival (50%). No differences between viruses were noted.ConclusionsExogenous p53 expression does not appear to increase the synergistic interaction of CRAds combined with radiotherapy. These results however do indicate that radiotherapy provides the time frame in which AdΔ24 and AdΔ24‐p53 can eradicate established tumors that would otherwise escape treatment, and establishes the need to combine these modalities to form an effective anti‐cancer treatment. Copyright © 2007 John Wiley & Sons, Ltd.
The impact of vertical resolution on regional model simulation of the west African summer monsoon
Authors: Druyan Leonard M. , Fulakeza Matthew , Lonergan Patrick 
Published: October 2007

AbstractThe RM3 regional climate model is used to simulate the west African summer monsoon for six June–September seasons using NCEP reanalysis data for lateral boundary forcing. The study compares the performance of the previously published 16‐level version with a newly tested 28‐level version, both running on a horizontal grid with 0.5° spacing, in order to determine what improvements in simulations are achieved by increased vertical resolution. Comparisons between the performances include diagnostics of seasonal mean precipitation rates and circulation, vertical profiles of cumulus heating rates, frequencies of shallow and deep convection and diagnostics related to transient African easterly waves (AEWs). The characteristics of a composite AEW simulated at both vertical resolutions are presented. Results show that the most significant impact of increasing the vertical resolution is stronger circulation, stronger vertical wind shear and higher amplitude AEWs. The simulations with higher vertical resolution also achieve higher peaks of cumulus latent heating rates. Spatial–temporal correlations between simulated daily 700 mb meridional winds versus corresponding NCEP reanalysis data and simulated daily precipitation versus estimates from the Tropical Rainfall Measurement Mission (TRMM) archive were equally high at both vertical resolutions. Copyright © 2007 Royal Meteorological Society
Programmable cells of monocytic origin (PCMO): A source of peripheral blood stem cells that generate collagen type II‐producing chondrocytes
Authors: Pufe Thomas , Petersen Wolf , Fändrich Fred , Varoga Deike , Wruck Christoph J. , Mentlein Rolf , Helfenstein Andreas , Hoseas Daniela , Dressel Stefanie , Tillmann Bernhard , Ruhnke Maren 
Published: October 2007

AbstractThe focus of this study was a new adult pluripotent cell derived from human peripheral blood monocytes identified as a “programmable cell of monocytic origin” (PCMO). In contrast to bone marrow‐derived stem cells, these cells can be harvested from peripheral venous blood without aspiration of the bone marrow and have multilineage potential comparable to that of mesenchymal stem cells (MSC). The aim of this study was to evaluate the potential of PCMOs to differentiate into collagen type II‐producing chondrocytes using various extrinsic cues (TGFβ‐1, IGF‐1, BMP‐2, and BMP‐7). Collagen type I and II proteins were localized using immunohistochemistry and quantified by enzyme‐linked immunosorbent assays (ELISA). The shape of the differentiating PCMOs was monitored with electron microscopy. Collagen type I and II messenger RNA expression was analyzed using real‐time reverse transcriptase‐polymerase chain reaction (RT PCR) and regular RT PCR. Immunohistochemistry revealed a strong accumulation of collagen type II after a 6‐week incubation period with BMP‐2, BMP‐7, TGF‐β, IGF‐I, and TGF‐β, and IGF‐1. Collagen type I was only mildly induced by the applied stimulants. Electron microscopy findings showed a shift from a monocyte‐like structure to a chondrocyte‐like structure after 2 weeks of stimulation. Stimulation of PCMOs with BMP‐2, BMP‐7, TGF‐β, IGF‐I, and TGF‐β, and IGF‐1 induced a chondrogenic differentiation with continuous expression of collagen type II mRNA and protein over several weeks time. Collagen type I and II expression in undifferentiated PCMOs or in control cells incubated without any stimulant was not detected. PCMOs have the potential to differentiate into collagen type II synthesizing chondrocytes. The ability to reprogram and differentiate PCMOs from peripheral blood into sizable quantities might enable their clinical application in cartilage repair after mechanical injury or in cases of osteoarthritis. © 2007 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 26:304–313, 2008