bluuebunny/crossref_metadata_2025_split huggingface dataset:
Towards an Integrated Description of Hydrogen Bonding and Dehydration: Decreasing False Positives in Virtual Screening with the HYDE Scoring Function
Authors: Reulecke Ingo , Lange Gudrun , Albrecht Jürgen , Klein Robert , Rarey Matthias 
Published: April 2008

AbstractWe developed a new empirical scoring function, HYDE, for the evaluation of protein–ligand complexes. HYDE estimates binding free energy based on two terms for dehydration and hydrogen bonding only. The essential feature of this scoring function is the integrated use of log P‐derived atomic increments for the prediction of free dehydration energy and hydrogen bonding energy. Taking the dehydration of atoms within the interface into account shows that some atoms contribute favorably to the overall score, while others contribute unfavorably. For instance, hydrogen bond functions are penalized if they are dehydrated unless they can overcompensate this loss by forming a hydrogen bond with excellent geometry. The main stabilizing contribution represents the removal of apolar groups from the water: the hydrophobic effect. Initial studies using the DUD dataset show that with HYDE, there is a significant decrease in false positives, a reasonable categorization of compounds as either non‐binders, weak, medium or strong binders, and in particular, there is a generally applicable and thermodynamically sensible cutoff score below which there is a high likelihood that the compound is indeed a binder.
Microarray‐Based Detection of Dye‐Labeled DNA by SERRS Using Particles Formed by Enzymatic Silver Deposition
Authors: Hering Katharina Konstanze , Möller Robert , Fritzsche Wolfgang , Popp Jürgen 
Published: April 2008

AbstractThe growing interest in DNA diagnostics is addressed today by microarrays with fluoresence detection. In our approach, we utilize spatially defined arrays of short oligonucleotides on a modified glass surface. Surface enhanced resonance Raman scattering (SERRS) is used to obtain molecularly specific spectra of the Raman‐active dye‐labeled DNA. Nanoparticles produced by enzymatic silver deposition are used as SERS‐active substrate. They grow directly on the modified oligonucleotides and only in the spatially defined areas on the chip. Furthermore, they potentially offer several advantages for SERS detection. The nanoparticles are characterized and their ability for use as SERS‐ and SERRS‐active substrate is estimated. Three different Raman‐active dyes are investigated for their potential for involvement in sequence specific DNA analysis.
The Cu7Sc Cluster is a Stable σ‐Aromatic Seven‐Membered Ring
Authors: Höltzl Tibor , Janssens Ewald , Veldeman Nele , Veszprémi Tamás , Lievens Peter , Nguyen Minh Tho 
Published: April 2008

AbstractDensity functional theory calculations demonstrate that the global minimum of the Cu7Sc potential energy surface is a seven‐membered ring of copper atoms with scandium in its center, yielding a planar D7h structure. Nucleus‐independent chemical shifts [NICS(1)zz and NICS(2)zz] show that this cluster has aromatic character, which is consistent with the number of 4s electrons of copper and scandium plus the 3d electrons of scandium satisfying Hückel’s rule. According to a canonical MO decomposition of NICS(1)zz and NICS(2)zz, the MOs consisting of the 4s atomic orbitals are mainly responsible for the aromatic behavior of the cluster. The electron localizability indicator (ELI–D) and its canonical MO decomposition (partial ELI–D) suggest that a localized basin is formed in Cu7Sc by the copper atoms whereas the two circular localized domains are situated below and above the ring. The planar Cu7Sc cluster can thus be considered as a σ‐aromatic species. These findings agree with the phenomenological shell model.
Preparation of Pd‐Based Metal Monolithic Catalysts and a Study of Their Performance in the Catalytic Combustion of Methane
Authors: Yin Fengxiang , Ji Shengfu , Wu Pingyi , Zhao Fuzhen , Liu Hui , Li Chengyue 
Published: April 2008

AbstractA series of Pd/SBA‐15/Al2O3/FeCrAl and Pd/5 wt % Ce1−xZrxO2/SBA‐15/Al2O3/FeCrAl (x=0–1) metal monolithic catalysts were prepared and characterized by various techniques. The catalytic activity and the stability of the catalysts for methane combustion were evaluated. All the catalysts retain the SBA‐15 mesoporous structure, with PdO being confined in its channels. The results show that the addition of Ce1−xZrxO2 as promoters can improve the activity and stability of the catalysts. The stabilities of the metal monolithic catalysts are much better than those of Pd/SBA‐15 particle catalysts. The catalyst with ZrO2 as promoter exhibits the best activity and stability (T90=395 °C), and the conversion of methane remains constant during the 700 h test.
Levels of adiponectin, C‐reactive protein and interleukin‐1 receptor antagonist are associated with insulin sensitivity: a population‐based study
Authors: Saltevo J. , Laakso M. , Jokelainen J. , Keinänen‐Kiukaanniemi S. , Kumpusalo E. , Vanhala M. 
Published: April 2008

AbstractBackgroundWe evaluated the relationship of insulin sensitivity (assessed with the quantitative insulin sensitivity check index, QUICKI) to adiponectin and pro‐inflammatory markers, levels of high‐sensitivity C‐reactive protein (hs‐CRP) and interleukin‐1 receptor antagonist (IL‐1 Ra).MethodsCross‐sectional study. Study population (N = 923, i.e 411 men and 512 women) included five different population‐based age groups (born in 1942, 1947, 1952, 1957 and 1962), [mean age 46 years and mean body mass index (BMI) 26 kg/m2]. Study protocol included an interview and measurements of anthropometric parameters and glucose, insulin, adiponectin, hs‐CRP and IL‐1 Ra.ResultsCorrelation (r) between QUICKI and adiponectin level was 0.334 [95% confidence intervals (CI), 0.275–0.392] and partial correlation adjusted for gender, BMI, smoking status, physical activity and age was 0.247 (95% CI, 0.185–0.308). There was negative correlation between QUICKI and IL‐1 Ra (r = − 0.385; 95% CI, − 0.440 to − 0.328) which remained statistically significant after the adjustment for confounding factors (r = − 0.178; 95% CI, − 0.240 to − 0.113). Similarly, QUICKI was negatively correlated with hs‐CRP (r = − 0.241; 95% CI, − 0.302 to − 0.178), but after the adjustment it lost its statistical significance. There was a statistically significant gender difference (p = 0.018) in correlation between QUICKI and IL‐1 Ra levels (men: r = − 0.348; 95% CI, − 0.436 to − 0.261; women r = − 0.500; 95% CI, − 0.537 to − 0.398).ConclusionsOur results show that adiponectin level and markers of low‐grade inflammation are related to insulin sensitivity. Adiponectin and IL‐1 Ra levels might be better markers of the risk of obesity and type 2 diabetes than hs‐CRP. Copyright © 2008 John Wiley & Sons, Ltd.
Benfotiamine exhibits direct antioxidative capacity and prevents induction of DNA damage in vitro
Authors: Schmid Ursula , Stopper Helga , Heidland August , Schupp Nicole 
Published: April 2008

AbstractBackgroundComplications in diabetes mellitus are partially mediated by enhanced formation of reactive oxygen species. Among the factors involved in reactive oxygen species formation, advanced glycation end products play a key role. Owing to a reduced activity of the enzyme transketolase, which requires diphosphorylated thiamine (vitamin B1) as cofactor, an accumulation of those deleterious glucose metabolites especially in diabetic patients can be observed. Benfotiamine, a lipophilic thiamine diphosphate prodrug, prevented early renal and retinal changes in animal studies, and reduced neuropathic pain in clinical studies. Several mechanisms for these activities have been described. We investigated for the first time direct antioxidant abilities of benfotiamine. Additionally, a potential DNA protective effect of benfotiamine was analysed.MethodsOxidative stress was detected by flow cytometry, antioxidative capacity was measured with the ferric reducing ability of plasma (FRAP) assay, two endpoints for genomic damage were assessed: the comet assay and the micronucleus test, and the expression and activity of transketolase was quantified.ResultsBenfotiamine prevented oxidative stress induced by the mutagen 4‐nitroquinoline‐1‐oxide (NQO), the uremic toxin indoxyl sulfate, and the peptide hormone angiotensin II in three different kidney cell lines. Cell‐free experiments showed a direct antioxidant effect of benfotiamine, which might account for the protective effect. Oxidative DNA damage, induced by angiotensin II, was completely prevented by benfotiamine. Incubation with benfotiamine increased transketolase expression and activity in the cells.ConclusionsBenfotiamine shows a direct antioxidant action. This effect of benfotiamine may be involved in the improvement of diabetic late complications, including peripheral neuropathy. Copyright © 2008 John Wiley & Sons, Ltd.
Modeling the moisture sorption isotherms of two‐phase solid olive oil by‐product
Authors: Liébanes María D. , Aragón Jose M. , Palancar María C. 
Published: April 2008

AbstractThe moisture sorption isotherms of two‐phase solid olive oil mill by‐product (SOB) were measured at different temperatures (15–50 °C) in order to thoroughly know the hygroscopic properties of this material. SOB is like a slurry with a high water content (60–70%). It is obtained in the olive oil two‐phase extraction process and is currently used as the raw material for obtaining pomace oil by extraction with hexane; prior to the extraction, drying of the SOB is required. Other uses of SOB are composting, animal feeding and solid fuel; in such cases, the previous drying of the material is also required. Sorption moisture isotherms for the two‐phase SOB were obtained by a static method. Eight models were fitted to the experimental data: BET, GAB, Halsey, Smith, Henderson, Oswin, Ferro‐Fontan and Peleg. The GAB equation was the best option to describe the water sorption behavior of SOB within a very wide range of water activities (0–0.90). A generalized GAB model, in which temperature is taken into account, was obtained by multivariable fitting of the complete set of the experimental isotherms.
Serinolic Amino‐s‐triazines: Iterative Synthesis of N‐Substituted Amino‐1,3‐dioxane Derivatives from l‐(p‐Nitrophenyl)serinols and Rotational Stereochemistry Phenomena
Authors: Fazekas Marijana , Pintea Monica , Lameiras Pedro , Lesur Amandine , Berghian Camelia , Silaghi‐Dumitrescu Ioan , Plé Nelly , Darabantu Mircea 
Published: April 2008

AbstractWe report the first iterative and chemioselective approach towards the synthesis of highly elaborated N‐substituted 2,4,6‐triamino‐s‐triazines (melamines) and precursors, by amination of cyanuric chloride with anancomeric and enantiomerically pure primary and tertiary amino‐1,3‐dioxanes. The starting nucleophiles were prepared by direct diastereospecific and diastereoselective acetalization of N‐substituted (1S,2S)‐2‐amino‐1‐(p‐nitrophenyl)propane‐1,3‐diols [l‐(p‐nitrophenyl)serinols]. The stereochemistry of the title compounds is discussed in terms of (pro)diastereomerism originating from restricted rotation about the newly created C(s‐triazine)–N< bonds and supported by NMR and DFT calculation data.(© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2008)
Enantio‐ and Diastereotopos Differentiation in the Palladium(II)‐Catalyzed Hydrosilylation of Bicyclo[2.2.1]alkene Scaffolds with Silicon‐Stereogenic Silanes
Authors: Rendler Sebastian , Fröhlich Roland , Keller Manfred , Oestreich Martin 
Published: April 2008

AbstractThe palladium(II)‐catalyzed hydrosilylation of meso‐configured bicyclo[2.2.1]alkene scaffolds proved to be an invaluable model reaction for the development of reagent‐controlled asymmetric transformations based on silicon‐stereogenic silanes as stereoinducers. In the present investigation, the subtle structural requirements of the silane substitution pattern in enantiotopos‐differentiating single hydrosilylations of a norbornene‐type substrate are disclosed. Extension of this chemistry to a double hydrosilylation of norbornadiene entails a significant increase in stereochemical complexity. Although differentiation of enantiotopic positions by the chiral reagent is demanded in the first hydrosilylation, the same reagent must then differentiate diastereotopic positions in the second. Remarkably high stereocontrol was found in this double hydrosilylation with several silanes first used in the hydrosilylations of the norbornene‐type system. Depending on the enantiomeric purity of the silane, C2‐ and Cs‐symmetric adducts, respectively, were obtained. The identity of the key quaternary silanes was revealed by crystallographic analysis. By this method, the relative and absolute configurations were also assigned, which, in turn, imply that all enantiospecific substitutions at silicon proceed with stereoretention. On the basis of these solid‐state structures, we also discuss the structural implications of silane substitution for the diastereoselectivity‐determining step of this palladium(II)‐catalyzed hydrosilylation reaction. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2008)
Regioselective and Stereospecific Halosilylating Cleavage of the Oxirane System of Glycidol Derivatives as an Efficient Strategy to C2‐O‐Functionalized C3‐Vicinal Halohydrins
Authors: Stamatov Stephan D. , Stawinski Jacek 
Published: April 2008

AbstractGlycidyl esters and ethers undergo a regioselective andstereospecific opening of the oxirane ring upon treatment with trimethylsilyl halides (TMSX, X = Cl, Br, or I) in the presence of pyridine to produce the corresponding C2‐O‐trimethylsilyl‐3(1)‐halo‐sn‐glycerols in high yields. Trifluoroacetylation across the trimethylsilyloxy system of such C3‐synthons with trifluoroacetic anhydride (TFAA) in the presence of a halide anion (e.g. Bu4NX; X = Cl, Br, or I), followed by removal of the trifluoroacetyl transient protection, provides nearly quantitative access to the respective vicinal haloalkanols. Alternatively, C2‐O‐acylated vicinal halohydrins can be obtained in a highly chemo‐/regiospecific manner by direct conversion of the trimethylsilyl protecting group into short‐ or long‐chain ester functionalities by means of a three‐component reagent: pyridine–carboxylic acid–TFAA. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2008)
Macrocyclic 14‐Membered Ring Diketal Diamines: Synthesis, Conformational Analysis and 99mTc Radiolabeling Evaluation (Eur. J. Org. Chem. 12/2008)
Authors: Affani Radouane , Auzeloux Philippe , Madelmont Jean‐Claude , Dugat Denise 
Published: April 2008

AbstractThe cover picture shows a rapid approach to new macrocyclic, 14‐membered ring diketal diamines, obtained by reduction of the corresponding diketal dilactams previously synthesized in two steps from chiral or achiral β‐amino alcohols. For these diamino compounds, the conformers of lower energy are either set in a strain‐free rectangular [3434]‐type structure or stabilized by two intramolecular NH···O hydrogen bonds, depending on the nature of the R1, R2 substituents and on the stereochemistry of the OMe groups. Details are discussed in the article by D. Dugat et al. on p. 2039 ff. Lionel Nauton is acknowledged for his help in the design of the cover picture.
A novel approach for analysis of oligonucleotide–cisplatin interactions by continuous elution gel electrophoresis coupled to isotope dilution inductively coupled plasma mass spectrometry and matrix‐assisted laser desorption/ionization mass spectrometry
Authors: Brüchert Wolfram , Krüger Ralf , Tholey Andreas , Montes‐Bayón María , Bettmer Jörg 
Published: April 2008

AbstractIn this work we present a novel approach for in vitro studies of cisplatin interactions with 8‐mer oligonucleotides. The approach is based on the recently developed coupling of continuous elution gel electrophoresis (GE) to an inductively coupled plasma‐sector field mass spectrometer (ICP‐SFMS) with the aim of monitoring the interaction process between this cytostatic drug and the nucleotides. In contrast to existing methods, the electrophoretic separation conditions used here allow both the determination of the reaction kinetics in more detail as well as the observation of dominant intermediates. Two different nucleotides sequences have been investigated for comparison purposes, one containing two adjacent guanines (5′‐TCCGGTCC‐3′) and one with a combination of thymine and guanine (5′‐TCCTGTCC‐3′), respectively. In order to gain further structural information, MALDI‐TOF MS measurements have been performed after fraction collection. This allows for identification of the intermediates and the final products and confirms the stepwise coordination of cisplatin via monoadduct to bisadduct formation. Furthermore, the ICP‐MS results were quantitatively evaluated in order to calculate the kinetics of the entire process.
Recent advances in surface‐enhanced Raman scattering detection technology for microfluidic chips
Authors: Chen Lingxin , Choo Jaebum 
Published: April 2008

AbstractMicrofluidic chip devices and their application to sensitive chemical and biological analyses have attracted significant attention over the past decade. The miniaturization of reaction systems offers practical advantages over conventional benchtop systems. In this case, however, a highly sensitive on‐chip detection method is important for the monitoring of chemical reactions as well as for the detection of analytes inside the channel because the detection volume in a micrometer‐size channel is extremely small. Recently, a surface‐enhanced Raman scattering (SERS) technique is being regarded as a potential candidate for the highly sensitive detection of analytes in a microfluidic chip. This review provides a general survey and an in‐depth look at recent developments in SERS techniques for the biological/environmental analysis of minute analytes in a microfluidic chip.
Chemical cytometry on microfluidic chips
Authors: Yan Hui , Zhang Boyang , Wu Hongkai 
Published: April 2008

AbstractChemical cytometry, referring to the analysis of the chemical contents in individual cells, has been in intensive study since Kennedy's first work that was published in Science. The early researches relied on fine‐tip capillaries to capture the cells and do the analyses, which were lab‐ and time‐intensive and required high skills of operation. The emergence of microfluidics has greatly spurred this research field and a great number of research papers have been published in the last decades. Highly integrated microfluidic chips have been developed to capture multiple single cells, lyse them, perform chemical reactions in enclosed microchambers, separate contents by CE and detect chemical species in individual cells. This review focuses on the development of relevant components and their integration for on‐chip chemical cytometry.
Cationized hydroxyethylcellulose as a novel, adsorbed coating for basic protein separation by capillary electrophoresis
Authors: Yang Runmiao , Shi Ronghua , Peng Shuhua , Zhou Dan , Liu Hang , Wang Yanmei 
Published: April 2008

AbstractWe present cationized hydroxyethylcellulose (cat‐HEC) synthesized in our laboratory as a novel physically adsorbed coating for CE. This capillary coating is simple and easy to obtain as it only requires flushing the capillary with polymer aqueous solution. A comparative study with and without polymers was performed. The adsorbed cat‐HEC coating exhibited minimal interactions with basic proteins, providing efficient basic protein separations with excellent reproducibility. Under broad pHs, the amine groups are the main charged groups bringing about a global positive charge on the capillary wall. As a consequence, the cat‐HEC coating produced an anodal EOF performance. A comparative study on the use of hydroxyethylcellulose (HEC) and cat‐HEC as physically adsorbed coatings for CE are also presented. The separation efficiency and analysis reproducibility proved that the cat‐HEC polymer was efficient in suppressing the adsorption of basic proteins onto the silica capillary wall. The long‐term stability of the cat‐HEC coating in consecutive protein separation runs has demonstrated the suitability of the coating for high‐throughput electrophoretic protein separations.
Improving sensitivity by large‐volume sample stacking combined with sweeping without polarity switching by capillary electrophoresis coupled to photodiode array ultraviolet detection
Authors: Zhang Huige , Zhou Lei , Chen Xingguo 
Published: April 2008

AbstractAn easy, simple, and highly efficient on‐line preconcentration method for polyphenolic compounds in CE was developed. It combined two on‐line concentration techniques, large‐volume sample stacking (LVSS) and sweeping. The analytes preconcentration technique was carried out by pressure injection of large‐volume sample followed by the EOF as a pump pushing the bulk of low‐conductivity sample matrix out of the outlet of the capillary without the electrode polarity switching technique using five polyphenols as the model analytes. Identification and quantification of the analytes were performed by photodiode array UV (PDA) detection. The optimal BGE used for separation and preconcentration was a solution composed of 10 mM borate–90 mM sodium cholate (SC)–40% v/v ethylene glycol, without pH adjustment, the applied voltage was 27.5 kV. Under optimal preconcentration conditions (sample injection 99 s at 0.5 psi), the enhancement in the detection sensitivities of the peak height and peak area of the analytes using the on‐line concentration technique was in the range of 18–26‐ and 23–44‐fold comparing with the conventional injection mode (3 s). The detection limits for (−)‐epigallocatechin (EGC), (−)‐epicatechin (EC), (+)‐catechin (C), (−)‐epigallocatechin gallate (EGCG), and (−)‐epicatechin gallate (ECG) were 4.3, 2.4, 2.2, 2.0, and 1.6 ng/mL, respectively. The five analytes were baseline‐separated under the optimum conditions and the experimental results showed that preconcentration was well achieved.
“Electrokinetic Analyte Transport Assay” for α‐fetoprotein immunoassay integrates mixing, reaction and separation on‐chip
Authors: Kawabata Tomohisa , Wada Henry G. , Watanabe Mitsuo , Satomura Shinji 
Published: April 2008

AbstractA rapid and highly sensitive CE immunoassay method integrating mixing, reaction, separation, and detection on‐chip is described for the measurement of α‐fetoprotein (AFP), a liver cancer marker in blood. Antibody‐binding reagents, consisting of 245‐bp DNA coupled anti‐AFP WA1 antibody (DNA‐WA1) and HiLyte dye‐labeled anti‐AFP WA2 antibody (HiLyte‐WA2), and AFP‐containing sample were filled into adjacent zones of a chip channel defined by the laminar flow lines of the microfluidic device using pressure‐driven flow. The channel geometry was thus used to quantitatively aliquot the reagents and sample into the chip. DNA‐WA1 was electrokinetically concentrated in the channel and sequentially transported through the AFP‐sample zone and HiLyte‐WA2 zone by ITP in such a manner that the AFP sandwich immune complex formation took place in the sample and HiLyte‐WA2 zones. The sandwich AFP immune complex was then detected by LIF after CGE in a separation channel that was arranged downstream of the reaction channel. AFP was detected within 136 s with a detection sensitivity of 5 pM. The on‐chip immunoassay described here, applying ITP concentration, in‐channel reaction, and CGE separation, has the potential of providing a rapid and sensitive method for both clinical and research applications.