bluuebunny/crossref_metadata_2025 huggingface dataset:
Paleocene deep-water depositional systems in the North Sea Basin
Authors: Dmitrieva Evelina , Jackson Christopher A-L. , Huuse Mads , McCarthy Adam
Published: March 2012

Interpretation of 3D seismic reflection data supported by well data provides insights into the geometry of early Paleogene depositional systems along the eastern margin of the North Viking Graben. These deposits, which consist mainly of sandstones interbedded with claystones and siltstones, are interpreted to document deposition at the edge of a large base-of-slope to proximal basin floor fan system which was sourced from the eastern basin margin. Individual sandstone bodies are up to 80 m thick and occur within four sandstone-prone packages (DU1–4), and well-to-seismic ties indicate that the thicker sandstones (>10 m) are represented by channelized or sheet-like, high-amplitude anomalies. Both well and seismic data suggest that the sandstones are of limited lateral extent (<1–5 km), implying they were deposited in a series of channels. Channelization and compensational stacking of sandstones may have been at least partly controlled by differential compaction across previously deposited sandbodies. The study reveals that deep-water depositional patterns are more complex than is apparent from previous, lithostratigraphically-driven correlations and from regional isochron mapping. In particular, this study has implications for the controls on the distribution and reservoir architecture of deep-water sandstones.
Burial diagenetic evolution of the Lower Carboniferous (Dinantian) of the southern margin of the Askrigg Platform and a comparison with the Derbyshire Platform
Authors: Hollis Cathy , Walkden Gordon
Published: March 2012

In order to predict the style and impact of post-depositional modification of carbonate successions, well-studied and accessible outcrop analogues are invaluable. The Lower Carboniferous (Dinantian) carbonate platforms of the Pennine Basin of northern England have a long history of investigation. As such, they offer the potential to evaluate the mechanisms and timing of fluid flux during extensional tectonism, post-rift basinal subsidence and inversion. This study concentrates upon the diagenetic evolution of the late Dinantian of the southern margin of the Askrigg Platform of North Yorkshire and a comparison with published data from the age-equivalent Derbyshire Platform. A pattern of consistent, diagenetic modification during early diagenesis is evident, but key differences occur in the burial realm. On both the southern margin of the Askrigg Platform and the Derbyshire Platform, patterns of dolomitization, hydrocarbon emplacement and mineralization can be determined on the platform that reflect the diagenetic evolution of the adjacent basins. However, within the study area of the Askrigg Platform, there is only local evidence for a fault/fracture control on the migration of Mg-enriched, hydrocarbon-bearing fluids. In contrast, on the Derbyshire Platform, burial diagenesis is intimately associated with NW–SE- and NE–SW-trending faults and fractures. Data suggest that pervasive cementation in the marine and meteoric realm occluded matrix porosity in both areas, such that fluid migration was almost entirely fracture controlled. With the localization of structural deformation along the Craven Fault Zone, and a low abundance and density of open fault/fracture networks, circulation of fluids on to the southern margin of the Askrigg Platform was inhibited, however. Furthermore, the presence of local aquifers in the Craven Basin may have led to fluid expulsion from the basin during early burial.
Error Diagnosis of Chinese Sentences Using Inductive Learning Algorithm and Decomposition-Based Testing Mechanism
Authors: Chang Ru-Yng , Wu Chung-Hsien , Prasetyo Philips Kokoh
Published: March 2012

This study presents a novel approach to error diagnosis of Chinese sentences for Chinese as second language (CSL) learners. A penalized probabilistic First-Order Inductive Learning (pFOIL) algorithm is presented for error diagnosis of Chinese sentences. The pFOIL algorithm integrates inductive logic programming (ILP), First-Order Inductive Learning (FOIL), and a penalized log-likelihood function for error diagnosis. This algorithm considers the uncertain, imperfect, and conflicting characteristics of Chinese sentences to infer error types and produce human-interpretable rules for further error correction. In a pFOIL algorithm, relation pattern background knowledge and quantized
t
-score background knowledge are proposed to characterize a sentence and then used for likelihood estimation. The relation pattern background knowledge captures the morphological, syntactic and semantic relations among the words in a sentence. One or two kinds of the extracted relations are then integrated into a pattern to characterize a sentence. The quantized
t
-score values are used to characterize various relations of a sentence for quantized
t
-score background knowledge representation. Afterwards, a decomposition-based testing mechanism which decomposes a sentence into background knowledge set needed for each error type is proposed to infer all potential error types and causes of the sentence. With the pFOIL method, not only the error types but also the error causes and positions can be provided for CSL learners. Experimental results reveal that the pFOIL method outperforms the C4.5, maximum entropy, and Naive Bayes classifiers in error classification.
Multiple testing in statistical analysis of systems-based information retrieval experiments
Authors: Carterette Benjamin A.
Published: March 2012

High-quality reusable test collections and formal statistical hypothesis testing together support a rigorous experimental environment for information retrieval research. But as Armstrong et al. [2009b] recently argued, global analysis of experiments suggests that there has actually been little real improvement in ad hoc retrieval effectiveness over time. We investigate this phenomenon in the context of simultaneous testing of many hypotheses using a fixed set of data. We argue that the most common approaches to significance testing ignore a great deal of information about the world. Taking into account even a fairly small amount of this information can lead to very different conclusions about systems than those that have appeared in published literature. We demonstrate how to model a set of IR experiments for analysis both mathematically and practically, and show that doing so can cause
p
-values from statistical hypothesis tests to increase by orders of magnitude. This has major consequences on the interpretation of experimental results using reusable test collections: it is very difficult to conclude that
anything
is significant once we have modeled many of the sources of randomness in experimental design and analysis.
ClickRank
Authors: Zhu Guangyu , Mishne Gilad
Published: March 2012

User browsing information, particularly non-search-related activity, reveals important contextual information on the preferences and intents of Web users. In this article, we demonstrate the importance of mining general Web user behavior data to improve ranking and other Web-search experience, with an emphasis on analyzing individual user sessions for creating aggregate models. In this context, we introduceClickRank, an efficient, scalable algorithm for estimating Webpage and Website importance from general Web user-behavior data. We lay out the theoretical foundation of ClickRank based on an intentional surfer model and discuss its properties. We quantitatively evaluate its effectiveness regarding the problem of Web-search ranking, showing that it contributes significantly to retrieval performance as a novel Web-search feature. We demonstrate that the results produced by ClickRank for Web-search ranking are highly competitive with those produced by other approaches, yet achieved at better scalability and substantially lower computational costs. Finally, we discuss novel applications of ClickRank in providing enriched user Web-search experience, highlighting the usefulness of our approach for nonranking tasks.
What It Means To Modernize
Authors: Tracey Ryan
Published: March 2012

Modernization means thinking differently about how you design learning environments. Not following the latest trends.
Azapentalenes. XLIV. 1H and 13C‐NMR study of mesoionic pyrazolo[1,2‐a]pyrazoles
Authors: Claramunt Rosa María , Trofimenko Sviatoslav , Rozas Isabel , Elguero José
Published: March 2012

The 1H and 13C chemical shifts as well as the 1H–1H and 1H–13C coupling constants of sixteen pyrazolo[1,2‐a]pyrazole derivatives have been measured. The most relevant features are discussed using resonance forms and simple additive models. AM1 semi‐empirical calculations have been carried out to provide a rationale for the NMR results.
Nitrogen NMR shieldings of 2‐amino‐5‐nitro‐6‐methylpyridines
Authors: Palasek B. , Puszko A. , Biedrzycka Z. , Sicinska W. , Witanowski M.
Published: March 2012

Nitrogen NMR shieldings (chemical shifts) of 2‐amino‐5‐nitro‐6‐methylpyridine derivatives are assessed from the point of view of substituent‐induced effects under conditions where alkyl, aryl, nitro, and nitroso moieties are substituents at the amino nitrogen. The nitro nitrogen shielding reveals only little variation upon varying the substituents, and this seems to indicate that steric hindrance which is likely to force the nitro group out of the plane of the aromatic ring reduces the π‐electron conjugation with the latter, and with the amino group as well. On the other side, the pyridine nitrogen shielding shows large effects of substituents at the amino moiety, which suggests a significant conjugation between the ring and the amino group. The latter effects produce a remarkable deshielding of the pyridine nitrogen in the case of nitro and nitroso substituents at the amino group.
Matrix‐assisted laser desorption ionization and electrospray ionization combined with Fourier transform ion cyclotron resonance mass spectrometry
Authors: Staneke Paul O. , Nibbering Nico M. M.
Published: March 2012

During recent years, matrix‐assisted laser desorption ionization (MALDI) and electrospray ionization (ESI) are successfully employed to analyze biomolecules and polymers. In combination with Fourier transform ion cyclotron resonance (FT‐ICR) mass spectrometry, high mass resolution and mass measurement accuracy can be achieved to enable the determination of molecular weights and structural characterization of biochemical compounds larger than 10 kDa.
Applications of artificial intelligence to structure determination of organic compounds. XX*. Determination of groups attached to the skeleton of natural products using 13C nuclear magnetic resonance spectroscopy
Authors: Rodrigues Gilberto do V. , Campos Ivan P. de Arruda , Emerenciano Vicente de P.
Published: March 2012

A procedure for the identification of substituent groups (viz. angelate, tiglate, etc.) attached to any of the atoms in the conventional skeleton of a natural product is described. It consists in the use of the program MACRONO, which was developed for finding subspectra due to the carbons in the said substituent groups amid the raw 13C NMR spectroscopic data from any given natural product (by means of comparisons of all possible subsets of the observed chemical shifts with those contained in an apposite database, built with literature 13C NMR spectroscopic data regarding those groups). This procedure enables one to expunge the chemical shifts not due to skeletal carbons from the initial dataset, which then can be input to the expert system SISTEMAT, for skeletal identification.
Bridge effect in charge transfer absorption bands of para‐substituted β‐nitrostyrenes
Authors: Morales Raúl G. E. , Vargas Victor , Hernández Carlos
Published: March 2012

Charge transfer electronic transitions in a series of para‐substituted β‐nitro‐styrenes are analyzed in order to characterize the π‐conduction channel between the electron‐donor substituents and the NO2 electron‐acceptor group, particularly the bridge effect of the olefinic molecular structure.

Absorption bands assignment of the π → π* electronic transitions in the near ultraviolet spectral region is carried out from an experimental and theoretical point of view. The photo‐induced charge transfer spectral bands of these aromatic compounds follow the same pattern as nitrobenzene, benzaldehyde and acetophenone and the electronic transition takes place in the π → π*(1La) excited state.

Our present study based on ZINDO/S‐CIS M.O. calculations permits us to analyse the role of the NO2 electron‐acceptor group, and the ethylenic group, where this last structure merges as a second electron‐acceptor group. The calculated olefinic bridge molecular resistivities (ρo) of these β‐nitrostyrenes range from 2.1 to 2.5 (Å/quantum).
Reactions of carboline
Authors: Dardonville Christophe , Virelizier Henri , Boivin Jean , Jankowski Christopher K.
Published: March 2012

The reactions of carboline under various oxidative conditions are reported. The soft aerobic radiolysis, hydroxylation and rearrangement transformations are studied using isotopic labelling and GC–MS techniques.
Use of 13C‐NMR as complementar identification tool in essential oil analysis
Authors: Alencar José Wilson , de Vasconcelos Silva Maria Goretti , Machado Maria Iracema Lacerda , Craveiro Afrânio Aragão , de Abreu Matos Francisco José , de Abreu Magalhães Ruy
Published: March 2012

A program using 13C‐NMR data was developed to improve GC/MS identifications of chemical constituents in essential oils. Compiled data uses 2290 and 2370 chemical shifts of 229 monoterpenes and 158 sesquiterpenes, respectively, stored into two reference libraries. Each carbon atom was codified using rules that correlates its chemical shift with structural features of the carbon hybridization and vicinity.
Total assignment of the 1H and 13C NMR spectra of piperovatine
Authors: Rendón Willy , Chávez Galia , Meléndez-Rodríguez Myriam , Joseph-Nathan Pedro
Published: March 2012

Total and unambiguous assignment of the 1H NMR spectrum of piperovatine [6‒(4‒methoxyphenyl)‒N‒(2‒methylpropyl)‒2,4‒hexadienamide] was carried out using conventional 1D NMR methods and spectral spin–spin simulation. Based on these data, the complete assignment of the 13C NMR chemical shift values was made by a 13C/1H chemical shift correlation diagram and conventional considerations for the quaternary carbon atom.
HR‐DOSY and sulfoxide enantiomeric discrimination by cyclodextrin
Authors: Borges Ricardo Batista , Laverde Antonio , Meleiro Porto André Luiz , Marsaioli Anita Jocelyne
Published: March 2012

Racemic and chiral ethyl‐phenylsulfoxide (solute) and β‐cyclodextrin (chiral selector) were used to compare two NMR methodologies to predict RP‐HPLC enantiomeric resolution efficiency. One of them based on the classical approach involving apparent binding constants and complexation‒induced chemical shifts at saturation and the other based on 13C NMR signal splittings (solute and chiral selector in stoichiometric ratio) and HR‐DOSY of the same solution. We have concluded that the latter methodology is rather efficient and though more elaborate from the NMR point of view, the results are promising and constitute an alternative method to investigate chiral recognition and other supramolecular phenomena.
Cyclization reactions of IMM‐125 and oxidation of cyclosporin A amino‐acid 1 in the α position of the double bond lead to the loss of in vitro immunosuppressive activity
Authors: Dieden R. , Latinne D. , Baldari C. , Maton N. , Aubry A. , Verbeeck R. K. , Zurini M. , Lhoëst G. J. J.
Published: March 2012

Cyclosporin A (CsA) and IMM‐125, a hydroxyethyl derivative of D‐serine CsA, are cyclic undecapeptides of molecular weight 1201.8 and 1261.8, respectively. The main metabolites still possessing the undecapeptide structure were found to be compounds resulting from the biotransformation of amino acids 4, 9 and 1.

Under the influence of the hepatic cytochrome P‐450‐dependent monooxygenase system, CsA and IMM‐125 amino acid 1 are metabolized to a mono‐hydroxylated compound (metabolite M‐17) and to a dihydrodiol. A metabolite M18 was found to be the result of a non‐enzymic intramolecular formation of a tetrahydrofuran derivative from metabolite M17. Since the existence of a CsA dihydrodiol was reported and since epoxides are considered as the dihydrodiol precursors, the aim of the present work was to prove that the same non‐enzymic intramolecular formation of a tetrahydrofuran ring could occur by nucleophilic attack of the amino‐acid 1 β‐hydroxy group at the ɛ‐position of the freshly formed epoxide by reaction of IMM‐125 with m‐chloro‐perbenzoic acid and cyclosporin A with selenium oxide. The immunosuppressive activity of the compounds, as measured by the mixed lymphocyte reaction and by the luciferase activity of a Jurkat‐T‐cell line stably transfected with the NF‐AT/luc reporter plasmid, was found negligible for IMM‐125 compared to the parent drug as well as for the cyclosporin A derivative. Structures of the IMM‐125 and CsA derivatives were elucidated by electrospray mass‒spectrometry and NMR spectroscopy.
Bridge effect of the C=C, C=N and N=N bonds on the long distance electronic charge transfer of para‒substituted stilbenoid compounds
Authors: Leiva Manuel A. , Morales Raul G. E.
Published: March 2012

By means of 13C‒NMR spectroscopy and ab initio molecular orbital theory calculations, we have analyzed the bridge effect of the C=C, C=N and N=N bonds on the long distance charge transfer of 4‒dimethylamino‒4′‒nitrostilbenoid compounds in the ground electronic state.

After a complete spectral assignment of the 13C‒NMR signals in these molecular compounds, we have characterized the effect of the nitrogen centres on the molecular bridge by means of the chemical shifts of the carbon centres, the theoretical charge densities and the dipolar moments.

From an electronic molecular point of view, our results describe two main properties of the double bond bridge. The first is related to the local charge accumulation capacity given by the type of the atomic centres and the structural orientation of the double bond bridge, and the second property is related to the modulation of the electronic charge distribution through the molecular system by the electrical polarization of the bridge.

Other complementary experimental evidences have permit us to establish new local molecular domains of the bridge effect in these stilbenoid compounds by means of linear correlations between 13C‒NMR chemical shifts of the aromatic carbon centres of the acceptor‒phenyl group and the molecular polarity of the species under study.
13C and 15N NMR shieldings of 1,2,4‐diazaphospholes in the solid state and in solution
Authors: Claramunt R.M. , López C. , Schmidpeter A. , Willhalm A. , Elguero J. , Alkorta I.
Published: March 2012

The solid state 13C and 15N CPMAS NMR spectra of 3,5‐di‐tert‐butyl‐1,2,4‐diazaphosphole 4 and 3,5‐diphenyl‐1,2,4‐diazaphosphole 5 have been recorded. The X‐ray structure of the first compound was already known (it is a cyclic dimer with localized N–H protons) while the structure of the second cannot be determined due to the difficulty to grow suitable single crystals. NMR results pointed out that 4 is a “classical” compound while 5 is probably a tetramer showing Intermolecular Solid‐State Proton Transfer (ISSPT). GIAO/ab initio calculations have been carried out to estimate the absolute 1H, 13C and 15N shieldings. The agreement with the experimental chemical shifts is good enough to assign the signals of carbons C‐3 and C‐5.
Vibrational spectroscopic studies of hydrogen‒bonded complexes between 2,5‐dihydroxy‐P‐benzoquinone and amines
Authors: Habeeb MoustafaM. , Al-Wakil Hoda A. , El-Dissouky Aly , Refat Nesrine M.
Published: March 2012

A series of 1 :1 hydrogen‐bonded complexes between 2,5‐dihydroxy‐P‐benzoquinone (DHBQ) and various nitrogen bases of different strengths were prepared. The FT‐IR spectra of the prepared complexes were examined in different regions. It has been found that the protonic and carbonyl vibrations are strongly affected by protonation. The intensity of protonic vibrations was estimated, the base line was corrected by using Perkin‐Elmer Paragon 1000 program. A maximum was found at pKa = 5.6 in the correlation between the intensity and pKa (amines) suggesting a critical behavior. The same value was located as a deep minimum in the correlation between the center of gravity of the protonic vibrations, vcg cm−1, and the pKa of the amines confirming the critical behavior in some of the studied complexes. The effect of the contribution of the second OH group to the IR absorption profile was discussed. Finally, the FT‐IR spectra of some deuterated complexes were presented and analysed.
NMR study of acutanol, a new cembrene alcohol, and sarcophytol A isolated from the soft coral Sarcophyton acutangulum
Authors: Mada Keiko , Ooi Takashi , Kusumi Takenori
Published: March 2012

A new cembrene alcohol, named acutanol, has been isolated from the soft coral, Sarcophyton acutangulum. Its structure has been determined on the basis of extensive NMR study. Absolute configuration of the major component, sarcophytol A, has been confirmed by use of a chiral anisotropic reagent, 1‒naphthylmethoxyacetic acid (1NMA).
FTIR and UV‒vis study of chemically engineered biomaterial surfaces for protein immobilization
Authors: Mansur Herman , Oréfice Rodrigo , Pereira Marivalda , Lobato Zélia , Vasconcelos Wander , Machado Lucas
Published: March 2012

The biomaterials research field has broadened in the last 3 decades, including replacement of diseased or damaged parts, assist in healing, correct and improve functional abnormality, drug delivery systems, immunological kits and biosensors. Proteins play crucial role in almost every biological system. They are involved in enzymatic catalysis, transport and storage, coordinated motion, mechanical support, immune protection, control of growth and cell differentiation among many others. The immobilization of proteins onto surface functionalized substrates has been one of the most promising areas in bioengineering field. It is important to note that the term immobilization can refer either to a temporary or to a permanent localization of the biomolecule on or within a support. Proteins have very particular chain configurations and conformations that promote high levels of specificity during chemical interactions. In the present work, we aimed to study the phenomenon of protein immobilization onto biomaterial with chemically engineered surface. We have tailored the surface of the porous gels of SiO2 with 5 different silane surface modifying agents: tetraethoxysilane (TEOS), 3‒mercaptopropyltrimethoxysilane (MPTMS) and 3‒aminopropyltriethoxysilane (APTES), 3‒glycidoxypropyltrimethoxysilane (GPTMS) and 3‒isocyanatopropyltriethoxysilane (ICPES). Fourier Transform Infrared Spectroscopy (FTIR) was used to characterize the presence of all specific chemical groups in the materials. The surface functionalized gels were then immersed in porcine insulin (PI) solutions for protein immobilization. The incorporation of protein within the gels was also monitored by FTIR spectroscopy. The kinetics of protein adsorption and desorption from the gel matrix in vitro tests were monitored by UV‒visible spectroscopy. We could not observe any evidence of denaturation of insulin after its desorption from gel matrices using UV‒visible spectroscopy technique. In vivo tests with adult male rats were used to verify the immobilized insulin bioactivity after implantation of different biomaterial with functionalized surfaces. Plasma glucose levels were obtained by using the Glucose GOD‒ANA Colorimetric Assay. All surface modified materials have presented acute hypoglycemic peak response associated with the insulin bioactivity.
Investigation of guanidine hydrochloride induced unfolding of apolipoprotein A‐IMilano
Authors: Suurkuusk Malin , Hallén Dan
Published: March 2012

A guanidine hydrochloride (GuHCl) induced unfolding study of apolipoprotein A‐IMilano (apo A‐IM) has been performed. The unfolding was followed by circular dichroism (CD) measurements at 222 nm and by isothermal titration (ITC) calorimetry at 25°C. In the ITC experiments enthalpies of transfer were determined for apo A‐IM from aqueous sodium phosphate buffer solution into solutions of different concentrations of GuHCl. The CD data and the ITC data give complementary and consistent results of the complex unfolding process. Analytical ultracentrifugation experiments were made on apo A‐IM in sodium phosphate buffer and in 0.6 M GuHCl, respectively. Analyses of the obtained sedimentation velocity data show that apo A‐IM is highly aggregated in sodium phosphate buffer. The aggregates are almost completely dissociated in 0.6 M GuHCl. Aggregation of the protein in sodium phosphate buffer solution induces an increase in α‐helical content. The loss of α‐helical secondary structural element of the protein upon dissociation of the aggregates destabilises the protein resulting in a low GuHCl concentration of unfolding, [GuHCl]m=1.1 M. The unfolded protein has a significant α‐helical content at the unfolded state. From ITC‐ and CD data we suggest that increased binding of GuHCl to the unfolded protein results in a disruption of the residual secondary structure.
Synchrotron radiation circular dichroism and conventional circular dichroism spectroscopy: A comparison
Authors: Lees J. G. , Wallace B. A.
Published: March 2012

Conventional circular dichroism (cCD) spectroscopy is a valuable tool for secondary structure analyses of proteins. In recent years, it has been possible to use synchrotrons as light sources for CD, with the technique being known as Synchrotron Radiation Circular Dichroism (SRCD). In this study, the spectra of two proteins, the primarily helical myoglobin and the primarily beta‒sheet concanavalin A, have been collected on both a cCD instrument and on the SRCD at the Daresbury synchrotron and their characteristics were compared. Over the wavelength regions where both instruments are capable of making measurements (from about 300 to 175 nm) the spectra are very similar, except at the low wavelength extreme of the cCD spectra. In this region, the spectra deviate somewhat, due to the limitations of the light source intensity in the conventional instrument. The SRCD spectra extend to much lower wavelengths (160 nm). This additional low wavelength vacuum ultraviolet (VUV) data contains a large amount of extra information, including, for the first time, a number of peaks consistent with previously predicted charge transfer transitions.
Driving Forces for the Adsorption of Enzymes at the Water/Silica Interface Studied by Total Internal Reflection Fluorescence Spectroscopy and Optical Reflectometry
Authors: Czeslik C. , Jackler G. , Royer C.
Published: March 2012

Total internal reflection fluorescence (TIRF) spectroscopy has been used to study conformational changes of hen egg white lysozyme induced by interaction with the water/quartz interface. TIRF spectra have been measured over a large temperature range and are compared to the corresponding solution spectra. It has been found that the wavelength of maximum fluorescence intensity of adsorbed lysozyme is red‐shifted by about 7 nm relative to that of dissolved lysozyme in the temperature range of about 20–60°C. This observation indicates that lysozyme is partially unfolding when it is adsorbing on quartz. Using optical reflectometry a drastic temperature‐induced increase of the degree of adsorption of lysozyme and staphylococcal nuclease (SNase) on silicon wafers has been measured which suggests that the corresponding adsorption processes are endothermic and thus entropically driven. The major contribution to this entropy gain will probably originate from conformational changes at lower temperatures. The experimental results indicate that proteins with a smaller Gibbs energy of unfolding have a higher tendency for adsorption. Above the temperatures of unfolding of the proteins in solution, the dehydration of hydrophobic residues, which are exposed to water in the thermally unfolded state, are the most likely driving force for the adsorption of lysozyme and SNase on silicon oxide.
Application of Different Lipid Surfaces to Monitor Protein–Membrane Interactions by Surface Plasmon Resonance Spectroscopy
Authors: Fischer Torsten , Senin Ivan I. , Philippov Pavel P. , Koch Karl-Wilhelm
Published: March 2012

Planar lipid bilayers on sensor chip surfaces have become useful tools to study membrane bound processes by surface plasmon resonance spectroscopy. We immobilized phospholipids on sensor chips by different approaches. First, a self‐assembled monolayer of octadecylmercaptan was formed on a blank gold surface and subsequent addition of phospholipids led to formation of a heterobilayer. Second, a self‐assembled monolayer of mercaptoundecanoic acid was formed on a gold surface, the carboxy groups of mercaptoundecanoic acid were activated and covalently linked to phosphatidylethanolamine. Addition of phospholipids then led to a bilayer with phosphatidylethanolamine as the lower leaflet. Third, a hydrophobic sensor chip (L1, BIAcore) was used as a binding matrix for phospholipids. These lipid surfaces were tested, whether they are suitable to study proteinamembrane interactions. As biological test system we used the Ca2+‐myristoyl‐switch of the neuronal Ca2+‐binding protein recoverin. All three surfaces were sufficiently stable to monitor the Ca2+‐dependent binding of recoverin to membranes.
A new system for detection of thermoluminescence and delayed luminescence from photosynthetic apparatus with precise temperature control
Authors: Noguchi Takumi , Katoh Masaya , Inoue Yorinao
Published: March 2012

A new system for thermoluminescence (TL) and delayed luminescence (DL) measurements with precise temperature control was developed. A freezing/heating stage for microscope was modified to afford a fixed sample temperature and a constant heating rate. A valve equipped with a low‒flow bypass for cold N2 gas through liquid N2 was used for both fine control of the sample temperature and for rapid cooling of the sample after flash illumination. High performance of the system was demonstrated by measurements of the TL glow curves with various heating rates and the DL decays at different temperatures arising from recombination of charged pairs in photosystem II membranes.
Heat, Cold and Pressure Induced Denaturation of Proteins
Authors: Panick G. , Herberhold H. , Sun Z. , Winter R.
Published: March 2012

We studied the pressureinduced unfolding and refolding of monomeric proteins, such as SNase, αchymotrypsin and ubiquitin, by using synchrotron Xray smallangle scattering and Fouriertransform infrared spectroscopy, which monitor changes in the tertiary and secondary structural properties of the proteins upon pressurization. Furthermore, by using the pressurejump relaxation technique in combination with timeresolved Xray diffraction and infrared spectroscopy, the kinetics of the unfolding/refolding of the proteins, was investigated. Significant differences in secondary structure and chain compactness in the folding/unfolding reactions of these proteins are observed. The results are compared with data obtained from other methods of denaturation, such as heat and pressure‐assisted cold denaturation. The cold‐ and pressure‐induced unfolding both yield a particularly unfolded state characterized by a persistent amount of secondary structure.
Spectroscopic Analysis of Amyloid Fibril Formation in SH3‐Domains
Authors: Ventura Salvador , Serrano Luis
Published: March 2012

The aggregation of proteins in fibrillar form is a problem of critical importance in a wide range of abnormal disease states. To decipher the molecular mechanism of formation of protein fibrillar aggregates we have chosen to study as model SH3 domains that exhibit different abilities to polymerize into amyloid fibrils. While being not related to any known disease, the SH3 domain of the p85α subunit of phosphatidylinositol 3 kinase has been found to form amyloid fibrils in vitro under acidic conditions, meanwhile, we have found that the spectrin SH3‒domain, sharing the same fold and some sequential identity keeps its native conformation under the same conditions. The use of spectroscopic methods to study these properties is illustrated in the present job, and correlated to direct sample observation by electron microscopy.
Clinical motivation for 31P MRS studies on the myocardial energy metabolism of brain dead cats
Authors: Bruinsma G. J. Brandon Bravo , Echteld C. J. A. Van
Published: March 2012

Hemodynamic instability of the brain dead potential heart donor is an exclusion criterion for heart donation for transplantation. Based on the results of myocardial biopsies it has been reported that brain death‐related catecholamine induced damage of the heart causes depletion of high‐energy phosphates which could explain contractile dysfunction. Our group has shown in a series of 31P MRS experiments in cats that neither the onset of brain death, nor the hemodynamic deterioration which follows, nor its treatment with high dosages of dopamine affect the heart energetically as expressed by PCr/ATP ratios. However, after cardioplegic arrest and explantation, an initial and prolonged lower ATP content and an anomalous higher PCr/ATP ratio in the brain death group was found when compared with controls during long‐term unperfused cold storage of the hearts. During subsequent reperfusion of the hearts, ATP and PCr levels in the brain death group were lower than in controls but equal partial recovery of PCr/ATP ratios was observed in both groups. It was concluded that PCr/ATP ratios need to be interpreted with great caution. Secondly, brain death‐related hemodynamic instability is not related to significant changes of myocardial energy metabolism. Thirdly, brain death does affect the myocardial energy metabolism but the impact became apparent only during hypothermic storage and subsequent reperfusion of the donor heart.
Neutron Inelastic Scattering as a High‐Resolution Vibrational Spectroscopy: New Tool for the Study of Protein Dynamics
Authors: Kataoka Mikio , Kamikubo Hironari , Nakagawa Hiroshi , Parker Stewart F. , Smith Jeremy C.
Published: March 2012

We have applied inelastic neutron scattering (INS) to the understanding of protein dynamics. INS spectrum of staphylococcal nuclease (SNase) at 25 K in the energy range between 100 and 4000 cm−1 is compared with the result of normal mode calculation. The theoretical spectrum is in general agreement with experiment and is used to assign the peaks. INS spectra show some significant differences for the folded and the unfolded SNase. The intensity distribution of INS spectrum is different from protein to protein reflecting the differences in amino acid composition. INS is unique and effective for the study of protein dynamics, especially for comparison with theory.
Thermal, chemical and chemothermal denaturation of yeast enolase
Authors: Huang Ping , Dong Aichun
Published: March 2012

We studied the temperature‒ and denaturant‒induced denaturation of yeast enolase by means of Fourier transform infrared spectroscopy. The temperature‒induced denaturation/aggregation of the enzyme in the absence of denaturant was highly cooperative and occurred between 55 and 65°C with a midpoint of ~58°C. Above 55°C, the intensity at 1656 cm−1 (predominantly α‒helix) decreases as a function of temperature, accompanied by the appearance of two new bands at 1622 and 1696 cm−1, indicating the formation of intermolecular β‒sheet aggregates. Five clearly defined isosbestic points were observed, indicating a two‒state conformational transition. Addition of a non‒denaturing concentration of gdnHCl (0.4 M) caused the thermal denaturation/aggregation of the enzyme to proceed faster, but this revealed no unfolding intermediate. The gdnHCl‒induced unfolding was first detected at a gdnHCl concentration of above 0.4 M, evidenced by loss of α‒helix and β‒sheet structures as functions of denaturant concentration. The fully unfolded state was reached at a gdnHCl concentration of 1.6 M. A significant amount of intermolecular β‒sheet aggregate was detected at gdnHCl concentrations between 0.6 and 1.0 M, which disappeared as the denaturant concentration increased further. The gdnHCl‒unfolded state is a heterogeneous ensemble of turns, helix/loops, and random structures, which continues to change at higher concentrations of denaturant.
Adsorption characteristics of albumin on gold and titanium metals in Hanks’ solution using EQCM
Authors: Lori J. A. , Hanawa T.
Published: March 2012

The adsorption of Bovine Serum Albumin (BSA) on gold and titanium surfaces in Hanks’ solution was monitored using the electrochemical quartz crystal microbalance (EQCM) technique. The changes in mass and open circuit potential at rest potential and mass and current at constant potentials were measured before and after the introduction of BSA.

The mass of BSA adsorbed on titanium reached a steady value within one hour, while the albumin adsorbed on gold continued to increase. The amount of BSA adsorbed by titanium increased with concentration and stabilized at 0.8 mg/ml while that on gold did not stabilize. This indicates a monolayer of the protein on titanium and multi‐layer on gold. The adsorption of BSA on gold and titanium was accelerated by the charge of potential.

The time before stabilizing the adsorption‒desorption phenomena also increased with the BSA concentration.
In situ FTIR assessment of dried Lactobacillus bulgaricus: KBr disk formation affects physical properties
Authors: Wolkers Willem F. , Oldenhof Harriëtte
Published: March 2012

The overall protein secondary structure, heat‒induced protein denaturation, membrane phase behaviour, and glassy behaviour of Lactobacillus bulgaricus dried with sucrose were studied by Fourier transform infrared spectroscopy (FTIR) using two sample preparation methods. Samples for FTIR analysis were either prepared by mixing dried sample with KBr and compression into disks or by air‒drying of cell/sucrose suspensions on CaF2 windows. The results show that KBr compression causes protein unfolding and affects the thermo‒physical properties of dried cells when compared with cells that were dried on CaF2 windows and directly used for FTIR analysis without further manipulation. The protein denaturation temperature of samples prepared in KBr disks was decreased by more than 70°C compared to that of samples dried on CaF2 windows. In addition, hydrogen bonding interactions of the glassy cell/sucrose matrix were drastically affected by KBr compression. In contrast with samples dried on CaF2 windows, samples in KBr disks were not in a glassy state at room temperature. The membrane phase behaviour of the dried cells was also affected by preparation of the sample into KBr disks. We conclude that the KBr compression method for preparing samples for FTIR analysis affects conformation and physical properties of biomolecules in the dried state.
A new method for studying platelets, based upon the low‐angle light scattering technique. 1. Theoretical and experimental foundations of the method
Authors: Mindukshev Igor V. , Jahatspanian Igor E. , Goncharov Nikolay V. , Jenkins Richard O. , Krivchenko Alexander I.
Published: March 2012

A new method is presented for simultaneous monitoring of changes in shape and aggregation of platelets. The signal of light scattering alterations at angles below six degrees was shown to be determined by platelet aggregation dynamics (aggregation, disaggregation, coagulation). Over a range of larger angles (6–15 degrees), cell shape changes also contributed to the signal: (i) spherization, and (ii) pseudopodia formation. The first stage was shown to be fast (t1/2 of few seconds) and correlated with [Ca2+] increase. It was characterised by a narrow signal fluctuation and by a rapid increase (30–40%) in signal intensity. During the second stage, which was much slower, the signal decreased describing the aggregation process. The EC50 value for ADP‐induced spherization was 40 nmol l–1. Aggregation kinetics in saline solution under turbulent flow showed second order kinetics in relation to initial cell concentration. The rate constant depended on stirring conditions and on calcium concentration in the medium. Standardisation of the testing conditions made it possible to characterize the initial functional state of platelets by their sensitivity to agonists, with estimation of EC50 and maximum velocity of aggregation (Umax) values. The method has potential applications in pharmacology and toxicology research and in clinical practice, as a simple and highly sensitive functionality test for platelets.
Quantitative oscillator analysis of IR‐optical spectra on spin‐cast chitosan films
Authors: Nosal W.H. , Thompson D.W. , Sarkar S. , Subramanian A. , Woollam J.A.
Published: March 2012

Infrared optical properties of spin‐cast chitosan films have been determined using spectroscopic ellipsometry. Infrared index of refraction and extinction coefficients from 750 cm–1 to 4000 cm–1 were determined using ellipsometric data fits to dispersion models based on Gaussian shaped oscillators. The free electron contribution was analyzed using a Drude model. This modeling determined that optical anisotropy was present over the entire infrared region. Line shape and oscillator strength analysis was performed to determine oscillator strengths, abundance, and relative bond strength.
On a novel dihalocyclopropane– dihalomethylvinyl rearrangement:Additional mechanistic evidence
Authors: Jankowski Christopher K. , BouLaouz Antoun , Diaz-Torres Eduardo
Published: March 2012

Some additional evidences on the mechanism of new rearrangment of dihalocyclopropane–dihalomethylvinyl reaction assisted by Hiyama reagent Cr+2/Cr+3 are discussed.
MALDI–TOF and FTIR microscopy analysis of blood serum from diarrhea patients
Authors: Huleihel Mahmoud , Karpasas Mark , Talyshansky Marina , Souprun Yelena , Doubijanski Yelena , Erukhimovitch Vitaly
Published: March 2012

Mass‒spectroscopic and vibrational spectroscopic methods were applied for the analysis of human blood samples from healthy subjects and patients in order to detect spectral peaks which might serve as biomarkers for monitoring and identification of specific diseases. In the present study samples of serum were obtained from healthy and patient persons suffering from diarrhea and analyzed by matrix‐assisted laser desorption/ionization time‐of‐flight (MALDI–TOF) and microscopic Fourier transform infrared spectroscopy (FTIR). The results obtained by both spectroscopic techniques show similar and consistent spectral peaks in all the examined sera obtained from healthy persons. In all tested patient samples two unique interesting peaks appeared at m/z 11,553 and 11,710 in MALDI‐TOF spectra and a peak at area 1600 cm−1 was significantly reduced in all of the tested patient samples in FTIR spectra. These parameters might be used as a basis for developing a spectral method for the detection and identification of specific human diseases and probably other disorders. It seems that a combination of these two techniques may provide much more reliable results for the detection and identification of various abnormalities.
A new method for studying platelets, based upon the low‐angle light scattering technique. 3. Aggregation hypersensitivity of platelets (ADP agonist) and search for corrective agents
Authors: Mindukshev Igor V. , Goncharov Nikolay V. , Shabanova Elena Yu. , Ermolaeva Elena E. , Mironova Maria O. , Radilov Andrey S. , Jenkins Richard O. , Krivchenko Alexander I.
Published: March 2012

A new method for studying platelets based on low‐angle light scattering has previously revealed that platelets taken from pregnant women with preeclampsia are hypersensitive to ADP, with aggregation developing at concentrations of 7–15 nmol l−1. The method has been applied to further studies in experimental toxicology and clinical pathology. Toxicological experiments with fluoroacetate (FA), an inhibitor of TCA cycle, showed that the platelet hypersensitivity could also be caused by energy depletion. In modeling experiments, the low‐angle light scattering method was applied to assessment of potential corrective agents of the pathological states related to hypersensitivity of platelets. Sodium glutamate (SG) was shown to be a potent antiaggregant in vitro, and subsequent in vivo studies demonstrated that SG can apparently serve as anaplerotic agent and normalize the platelet status of rats intoxicated with FA. Donators of nitric oxide (NO), such as isosorbide‐5′‐dinitrate, can also normalize in vitro the hypersensitive status of platelets taken from the patients with preeclampsia.
Hydroxyl radical induced structural changes of collagen
Authors: Xiao Helan , Cai Guoping , Liu Mingyao
Published: March 2012

Extracellular matrix (ECM) plays an important role in cell differentiation, growth, migration and apoptosis. Collagen is the most abundant protein family in vivo, but its function has still not been clearly defined yet. Reactive oxygen species (ROS) have a central role in oxidative cell stress. Electron spin resonance (ESR) spectroscopy indicates that type I collagen could uniquely scavenge hydroxyl radicals in dose‐ and time‐dependent manner; whereas BSA and gelatin (a denatured collagen) have no such an effect. However, the mechanism by which type I collagen scavenges hydroxyl radicals is different from that of GSH, a well‐known free radical scavenger. Using a new method, two‐dimensional FTIR correlation analysis, for the first time, we show that the order of functional group changes of type I collagen in this process is amide I earlier than amide II than amide III than –CH– than ν(C=O). The results indicates that the structure of the main chain of collagen changed first, followed by more residue group ν(C=O) exposed to hydroxyl radicals. The reaction with the carbonyl group in collagen causes the hydroxyl free radicals to be scavenged. Therefore, ECM can effectively scavenge ROS under normal physiological conditions. When the proteins of ECM were denatured in the same way as gelatin, they lost their function as a free radical scavenger. All of these results provide new insight into therapy or prevention of oxidative stress, apoptosis and ageing.
Necrotic and apoptotic volume changes of red blood cells investigated by low‐angle light scattering technique
Authors: Mindukshev Igor V. , Krivoshlyk Vladimir V. , Ermolaeva Elena E. , Dobrylko Irina A. , Senchenkov Evgeniy V. , Goncharov Nikolay V. , Jenkins Richard O. , Krivchenko Alexander I.
Published: March 2012

A low‐angle light scattering technique, which has been applied previously to studies of blood platelets and Ehrlich ascite tumor cells, revealed differences in the dynamics of necrotic and apoptotic red blood cell death. Under hypotonic loading or in ammonia medium, red blood cells (RBC) swelled to a critical size (diameter approximately 13 μm) prior to hemolysis (necrosis). Under acidic loading, hemolysis occurred with less pronounced swelling of cells (diameter approximately 10 μm). Apoptosis induced by a calcium ionophore resulted in initial formation of echinocytes, followed by development of rounded red blood cells with uneven membrane, capable of agglomeration. In such a way, RBC aggregation can precede the final stages of the RBC apoptosis when small cellular fragments are generated. On the basis of erythrograms of the cells hemolysing in ammonia medium, the echinocytic (preapoptotic) and stomatocytic (prenecrotic) RBC were discerned due to the very high resistance of apoptotic RBC to osmotic (ammonia) loading.
Synchrotron FT‐IR microspectroscopic analysis of necrotic bone
Authors: Bayarı Sevgi Haman , Utku Haluk , Ikemoto Yuka , Celasun Bülent , Kömürcü Mahmut , Atik Aziz
Published: March 2012

Avascular necrosis (osteonecrosis) is a disease that results from the temporary or permanent loss of blood supply to the bone. Synchrotron FT‐IR microspectroscopy has been used to study the changes in mineral and matrix content of necrotic bone. FT‐IR spectroscopic analysis revealed that in necrotic bone the relative mineral/matrix ratio decreased. Spectroscopic differences were observed between normal and necrotic bones. The noticeable differences may have important implications for analyzing and evaluating death bone.