bluuebunny/crossref_metadata_2025_split huggingface dataset:
Using grey dynamic modeling and pseudo amino acid composition to predict protein structural classes
Authors: Xiao Xuan , Lin Wei‐Zhong , Chou Kuo‐Chen 
Published: March 2008

AbstractUsing the pseudo amino acid (PseAA) composition to represent the sample of a protein can incorporate a considerable amount of sequence pattern information so as to improve the prediction quality for its structural or functional classification. However, how to optimally formulate the PseAA composition is an important problem yet to be solved. In this article the grey modeling approach is introduced that is particularly efficient in coping with complicated systems such as the one consisting of many proteins with different sequence orders and lengths. On the basis of the grey model, four coefficients derived from each of the protein sequences concerned are adopted for its PseAA components. The PseAA composition thus formulated is called the “grey‐PseAA” composition that can catch the essence of a protein sequence and better reflect its overall pattern. In our study we have demonstrated that introduction of the grey‐PseAA composition can remarkably enhance the success rates in predicting the protein structural class. It is anticipated that the concept of grey‐PseAA composition can be also used to predict many other protein attributes, such as subcellular localization, membrane protein type, enzyme functional class, GPCR type, protease type, among many others. © 2008 Wiley Periodicals, Inc. J Comput Chem 2008.
Raman spectroscopy of the nickel silicate mineral pecoraite—an analogue of chrysotile (asbestos)
Authors: Frost Ray L. , Jagannadha Reddy B. , Dickfos Marilla J. 
Published: March 2008

AbstractThe molecular structure of the mineral pecoraite, the nickel analogue of chrysotile of formula Ni3Si2O5(OH)4, was analysed by a combination of Raman and infrared spectroscopies. A comparison is made with the spectra of the minerals nepouite and chrysotile and a synthetic pecoraite. Pecoraite is characterised by OH stretching vibrations at 3645 and 3683 cm−1 attributed to the inner and inner surface hydroxyl stretching vibrations. Intense infrared bands at around 3288 and 3425 cm−1 are assigned to the stretching vibrations of water strongly hydrogen‐bonded to the surface of the pecoraite. The asbestos‐like mineral is characterised by SiO stretching vibrations at 979, 1075, 1128 and 1384 cm−1, OSiO chain vibrations at 616 and 761 cm−1 and NiO(H) vibrations at 397 and 451 cm−1. Copyright © 2008 John Wiley & Sons, Ltd.
Thermo‐Raman spectroscopy of synthetic nesquehonite — implication for the geosequestration of greenhouse gases
Authors: Hales Matthew C. , Frost Ray L. , Martens Wayde N. 
Published: March 2008

AbstractPure nesquehonite (MgCO3·3H2O)/Mg(HCO3)(OH)·2H2O was synthesised and characterised by a combination of thermo‐Raman spectroscopy and thermogravimetry with evolved gas analysis. Thermo‐Raman spectroscopy shows an intense band at 1098 cm−1, which shifts to 1105 cm−1 at 450 °C, assigned to the ν1CO32− symmetric stretching mode. Two bands at 1419 and 1509 cm−1 assigned to the ν3 antisymmetric stretching mode shift to 1434 and 1504 cm−1 at 175 °C. Two new peaks at 1385 and 1405 cm−1 observed at temperatures higher than 175 °C are assigned to the antisymmetric stretching modes of the (HCO3)− units. Throughout all the thermo‐Raman spectra, a band at 3550 cm−1 is attributed to the stretching vibration of OH units. Raman bands at 3124, 3295 and 3423 cm−1 are assigned to water stretching vibrations. The intensity of these bands is lost by 175 °C. The Raman spectra were in harmony with the thermal analysis data. This research has defined the thermal stability of one of the hydrous carbonates, namely nesquehonite. Thermo‐Raman spectroscopy enables the thermal stability of the mineral nesquehonite to be defined, and, further, the changes in the formula of nesquehonite with temperature change can be defined. Indeed, Raman spectroscopy enables the formula of nesquehonite to be better defined as Mg(OH)(HCO3)·2H2O. Copyright © 2008 John Wiley & Sons, Ltd.
The analysis of naturally and artificially aged protein‐based paint media using Raman spectroscopy combined with Principal Component Analysis
Authors: Nevin Austin , Osticioli Iacopo , Anglos Demetrios , Burnstock Aviva , Cather Sharon , Castellucci Emilio 
Published: March 2008

AbstractThe analysis of protein‐based paint media used in paintings is presented using micro‐Raman spectroscopy, carried out with a diode laser emitting at a wavelength of 785 nm. Following a contextualisation of the analysis and ageing of protein‐based binding media, a consideration of the effects of artificial ageing using visible light on the Raman spectra of binding media is given and the interpretation of changes to the Raman spectra of selected binding media is presented. Bands associated with aromatic amino acids are most affected by ageing, but spectra retain diagnostic information for the identification of proteins. Specific changes to the spectra of dairy and collagen‐based binding media are described and explained with reference to the oxidation of amino acids. A multivariate approach using Principal Component Analysis has been chosen for the assessment of the bands in CH stretching region for which a large set of over 150 spectra were recorded from artificially and naturally aged binding media which included egg white, egg yolk, milk and casein, and collagen‐based glues from rabbit skin, ox bone, parchment and sturgeon bladder. Raman spectroscopy has been used for an assessment of the effects of ageing and the detection of degradation due to exposure of light. Multivariate analysis has allowed the differentiation between a large data set of spectra of naturally and artificially aged binding media. Copyright © 2008 John Wiley & Sons, Ltd.
Polymorphism incidence in commercial tablets of mebendazole: a vibrational spectroscopy investigation
Authors: Ayala A. P. , Siesler H. W. , Cuffini S. L. 
Published: March 2008

AbstractMebendazole is a broad spectrum anthelminthic drug, which is widely used in large scale deworming programmes. This active pharmaceutical ingredient exhibits three crystal forms, namely, polymorphs A, B, and C. Therapeutic trials suggested that the most stable form, polymorph A, is inactive. However, the dissolution test normally used as a quality control tool is not able to discriminate among the polymorphs of mebendazole. In this work, the ability of the vibrational spectroscopic techniques (mid and nearinfrared absorption and Raman scattering) for the identification of the crystal form of this compound is evaluated. On the basis of these observations, this methodology is applied to determine the polymorphs of MBZ used in the formulation of the commercial tablets available in the Brazilian and German markets. Copyright © 2008 John Wiley & Sons, Ltd.
Resonance Raman studies of photochemical molecular devices for multielectron storage
Authors: Tschierlei Stefanie , Dietzek Benjamin , Karnahl Michael , Rau Sven , MacDonnell Frederick M. , Schmitt Michael , Popp Jürgen 
Published: March 2008

AbstractResonance Raman spectroscopy was utilized for the first time to characterize the nature of the 1metal‐to‐ligand charge transfer (MLCT) state of a ruthenium complex containing the redoxactive tetraazatetrapyrido‐pentacene (tatpp) ligand. The presented results show that the long‐wavelength absorption is originating from transitions involving the terminal phenanthroline and the tatpp ligands. Copyright © 2008 John Wiley & Sons, Ltd.
Raman spectroscopic study of the uranyl mineral, compreignacite, K2[(UO2)3O2(OH)3]2·7H2O
Authors: Frost Ray L. , Dickfos Marilla J. , Čejka Jiří 
Published: March 2008

AbstractRaman spectra of the uranyl oxyhydroxy‐hydrated mineral compreignacite, K2[(UO2)3O2(OH)3]2·7H2O, were measured and interpreted. Observed bands were attributed to the stretching and bending vibrations of uranyl units, molecular water and hydroxyl ions. UO bond lengths in uranyl and OHO hydrogen bond lengths were inferred from the spectra and compared with those from the X‐ray single crystal structure data. The importance of this spectroscopic study rests with the ability to analyze very small amounts of the mineral. Copyright © 2008 John Wiley & Sons, Ltd.
Lithium solvation in a PMMA membrane plasticized by a lithium‐conducting ionic liquid based on 1‐butyl‐3‐methylimidazolium bis(trifluoromethanesulfonyl)imide
Authors: Duluard Sandrine , Grondin Joseph , Bruneel Jean‐Luc , Campet Guy , Delville Marie‐Hélène , Lassègues Jean‐Claude 
Published: March 2008

AbstractThe Raman and Infrared (IR) spectra of poly(methyl methacrylate) (PMMA) membranes plasticized by ionic liquids of the (1 − x)[1‐butyl‐3‐methylimidazolium bis(trifluoromethanesulfonyl)imide (BMITFSI)],xLiTFSI type, where BMI+ is the 1‐butyl‐3‐methylimidazolium cation and TFSI− the bis(trifluoromethanesulfonyl)imide anion, are analyzed for a lithium bis(trifluoromethane sulfone)imide (LiTFSI) mole fraction x = 0.23 and PMMA contents from 0 to 50 wt%. The lithium is found to have an average coordination of about three CO groups and less than one TFSI− anion. It plays the role of a cross‐linker between the ester groups of PMMA and the nonvolatile ionic liquid. Addition of PMMA to the (1 − x)(BMITFSI),xLiTFSI ionic liquid lowers the conductivity but might improve the lithium transference number by transforming the [Li(TFSI)2]− anionic clusters present in the pure ionic liquid into a mixed coordination by ester groups and TFSI− anions. Copyright © 2008 John Wiley & Sons, Ltd.
Structural and chemical differences in the cell wall regions in relation to scale firmness of three onion (Allium cepa L.) selections at harvest and during storage
Authors: Coolong Timothy W , Randle William M , Wicker Louise 
Published: March 2008

AbstractBACKGROUND: Firmness in vegetables is an important textural attribute affecting consumer attitudes toward freshness and quality. Firmness, structural carbohydrates, polygalacturonase (PG), and pectin methylesterase (PME) activity were measured in three onion (Allium cepa L.) lines at harvest and after 4, 8, and 12 weeks of storage.RESULTS: The high‐dry‐matter onion, MBL87‐WOPL, had the firmest bulbs at harvest and delayed softening during storage. MBL87‐WOPL had the thickest cell wall/middle lamella region, and highest levels of dry matter and total uronic acid. Furthermore, MBL87‐WOPL had the lowest levels of PG and PME activity during storage. Pegasus, a poor‐storing cultivar, had the softest bulbs at harvest, lowest levels of uronic acid, and thinnest cell wall/middle lamella. A good storing, moderately firm onion cultivar (MSU4535B) presented intermediate levels of firmness and total uronic acid content. Differences in uronic acid in water‐soluble pectin accounted for much of the difference in total uronic acid among lines. Cellulose concentrations were similar among all lines at harvest. In addition, cellulose concentrations decreased in all lines during storage. Transmission electron microscopy performed on bulbs at harvest and after 12 weeks of storage indicated that degradation of the middle lamella had occurred during storage, leading to cell separation.CONCLUSION: Our results suggest that differences in onion scale firmness at harvest may be due to differences in water‐soluble pectin uronic acid concentrations. Furthermore, the rate of bulb softening during storage at 6.6 °C was greater in onion lines with higher levels of PME and PG activity in storage. Copyright © 2008 Society of Chemical Industry
Antioxidative capacity produced by Bifidobacterium‐ and Lactobacillus acidophilus‐mediated fermentations of konjac glucomannan and glucomannan oligosaccharides
Authors: Wang Cheng‐Hsin , Lai Phoency , Chen Mei‐En , Chen Hsiao‐Ling 
Published: March 2008

AbstractBACKGROUND: Konjac glucomannan (KGM) has been shown to stimulate the growth of bifidobacteria and lactobacilli in the human and rat colon. This study investigated the antioxidative effects produced after 48 h in vitro fermentation of unhydrolysed KGM and two hydrolysed KGM fractions (KH1 and KH2 with degree of polymerisation 10 and 5 respectively) by Bifidobacterium adolescentis, B. bifidum, B. breve, B. longum and Lactobacillus acidophilus respectively. The inhibitory effect on conjugated diene formation, ferric‐chelating capacity, α,α‐diphenyl‐β‐picrylhydrazyl (DPPH) radical‐scavenging ability and thiobarbituric acid‐reactive substances (TBARS) concentration produced by these fermentations were compared with those of oligofructose (OF) fermentation.RESULTS: The fermentation of KGM by each bacterial strain produced higher ferric‐chelating capacity of the culture supernatant compared with KH2 or OF fermentation. In contrast, the fermentation of KGM by each bacterial strain led to lower inhibition of conjugated diene formation and lower radical‐scavenging ability compared with KH2 fermentation. The fermentation of KH2 produced the lowest amount of TBARS.CONCLUSION: The fermentation of unhydrolysed KGM by colonic lactic acid bacteria in vitro produced antioxidative capacity mainly by preventing the initiation of ferrous ion‐induced peroxidation, whereas the fermentation of konjac oligosaccahrides did so by increasing the radical‐scavenging ability and eliminating lipid peroxide formation. Copyright © 2008 Society of Chemical Industry
Long‐term survival after radical prostatectomy compared to other treatments in older men with local/regional prostate cancer
Authors: Liu Liqian , Coker Ann L. , Du Xianglin L. , Cormier Janice N. , Ford Charles E. , Fang Shenying 
Published: March 2008

AbstractBackgroundThis study aimed to address long‐term survival in a large population‐based cohort of men with prostate cancer receiving radical prostatectomy compared to other treatments.MethodsWe studied 5,845 patients diagnosed with local/regional stage prostate cancer at age 65–74 in 1992 with comorbidity score <2, who were defined as potential candidates for radical prostatectomy and identified from the SEER (Surveillance, Epidemiology and End Results)‐Medicare cohort with median follow‐up of 11 years.ResultsOf 5,845 patients, 10‐year all‐cause survival rates were the highest for patients receiving radical prostatectomy (81.0%; 95% CI: 79.4–82.4%), followed by radical prostatectomy in combination with radiotherapy (67.6%; 62.0–72.5%), radiotherapy (60.5%; 58.3–62.6%), and were the lowest for watchful‐waiting (50.7%; 47.5–53.8%). A similar pattern was found for 10‐year prostate cancer‐specific survivals by treatments. After adjusting for age, ethnicity, region, Gleason Score, comorbidity, median annual household income, hormone therapy and chemotherapy, the hazard ratio of all‐cause mortality was 0.31 (95% CI: 0.25–0.37) for radical prostatectomy and 0.38 (95% CI: 0.28–0.52) for radical prostatectomy plus radiation therapy compared to those with watchful‐waiting.ConclusionsThere was a significant long‐term survival benefit in men receiving radical prostatectomy compared to those receiving watchful‐waiting or radiotherapy. J. Surg. Oncol. 2008;97:583–591. © 2008 Wiley‐Liss, Inc.
Syntheses and Comparison of 2,6‐Di‐O‐methyl Celluloses from Natural and Synthetic Celluloses
Authors: Kamitakahara Hiroshi , Koschella Andreas , Mikawa Yuji , Nakatsubo Fumiaki , Heinze Thomas , Klemm Dieter 
Published: March 2008

Abstract2,6‐Di‐O‐methylcellulose was prepared from natural and synthetic celluloses. Natural cellulose was converted to 2,6‐di‐O‐thexyldimethylsilylcellulose, then to 3‐mono‐O‐allyl‐2,6‐di‐O‐methylcellulose, and finally into 2,6‐di‐O‐methylcellulose. Alternatively, 2,6 di‐O‐methylcellulose was synthesized from the synthetic cellulose derivative 3‐mono‐O‐benzyl‐2,6‐di‐O‐pivaloylcellulose by depivaloylation and methylation to give 3‐mono‐O‐benzyl‐2,6‐di‐O‐methylcellulose, which was debenzylated to yield the dimethyl ether. Both types of 2,6‐di‐O‐methylcellulose are insoluble in water and common organic solvents. The structures of all cellulose derivatives were determined by NMR.magnified image
New Insights into Polylactide Biodegradation from Molecular Ecological Techniques
Authors: Sangwan Parveen , Wu Dong Yang 
Published: March 2008

AbstractMolecular ecological techniques for direct identification of microbes involved in PLA degradation under aerobic composting conditions are described. Gene sequences from genera Paecilomyces, Thermomonospora, and Thermopolyspora were most abundant in the compost samples. Members of these phylogenetic lineages are therefore likely to play an important role in PLA degradation. The use of molecular ecological techniques to design cultivation strategies may also provide a new tool for identification and investigation of biodegradation mechanisms and for future development of efficient biological treatment or recycling processes for PLA and other biodegradable polymers.magnified image
Electrochemically Active Block Copolymer Micelles Containing Coumarin Moieties
Authors: Dahmane Smail , Lasia Andrzej , Zhao Yue 
Published: March 2008

AbstractWe report the first study of using CPE to disrupt block copolymer micelles containing an organic chromophore. Micelles formed by an amphiphilic diblock copolymer composed of PEO and PCMA are electrochemically active in aqueous electrolyte solution, displaying an irreversible oxidation process of coumarin at a potential of about 1.75 V. CPE of the micellar solution at the fixed oxidation potential allows a large amount of coumarin moieties inside the hydrophobic micelle core to be electrochemically oxidized, resulting in the transformation of small polymer micelles (ca. 38 nm) onto larger aggregates (ca. 1 µm). This study demonstrates that electrochemical redox reactions can be explored as a means to disrupt block copolymer micelles that contain a light‐sensitive organic chromophore such as coumarin.magnified image
Stimuli‐Responsive Hybrid Coatings of Polyelectrolyte Multilayers and Nano‐Patterned Polymer Brushes
Authors: Yang Sung Yun , Kim Dul‐Yi , Jeong Sang‐Mi , Park Ji‐Woong 
Published: March 2008

AbstractA new type of polymeric hybrid coating is created by layer‐by‐layer deposition of polyelectrolyte multilayers (PEM) onto nano‐patterned polymer brushes (NPB). The PEM is a hydrogen‐bonded multilayer consisting of poly(acrylic acid) and poly(acrylamide) and the NPB is derived from a surface reactive rod‐coil block copolymer, polystyrene‐block‐poly[3‐(triethoxysilyl)propylisocyanate]. The thickness of the PEM coating is optimized with respect to the height of the NPB mounds, to yield PEM/NPB hybrid coatings with unique nano‐embossed or nano‐porous structures that can be interchangeable by heating and moisture annealing. The hybrid coating is patternable by the micro‐contact printing method. The results demonstrate that the combination of surface‐bound, hydrophobic NPB layer with hydrophilic PEM films at the nanoscopic level offers a new organic hybrid coating with novel surface properties.magnified image
A multi‐angular mass spectrometric view at cyclic nucleotide dependent protein kinases: In vivo characterization and structure/function relationships
Authors: Scholten Arjen , Aye Thin‐Thin , Heck Albert J.R. 
Published: March 2008

AbstractMass spectrometry has evolved in recent years to a well‐accepted and increasingly important complementary technique in molecular and structural biology. Here we review the many contributions mass spectrometry based studies have made in recent years in our understanding of the important cyclic nucleotide activated protein kinase A (PKA) and protein kinase G (PKG). We both describe the characterization of kinase isozymes, substrate phosphorylation, binding partners and post‐translational modifications by proteomics based methodologies as well as their structural and functional properties as revealed by native mass spectrometry, H/D exchange MS and ion mobility. Combining all these mass spectrometry based data with other biophysical and biochemical data has been of great help to unravel the intricate regulation of kinase function in the cell in all its magnificent complexity. © 2008 Wiley Periodicals, Inc. Mass Spec Rev 27: 331–353, 2008
Resveratrol directly targets COX‐2 to inhibit carcinogenesis
Authors: Zykova Tatyana A. , Zhu Feng , Zhai Xiuhong , Ma Wei‐Ya , Ermakova Svetlana P. , Lee Ki Won , Bode Ann M. , Dong Zigang 
Published: March 2008

AbstractTargeted molecular cancer therapies can potentially deliver treatment directly to a specific protein or gene to optimize efficacy and reduce adverse side effects often associated with traditional chemotherapy. Key oncoprotein and oncogene targets are rapidly being identified based on their expression, pathogenesis and clinical outcome. One such protein target is cyclooxygenase‐2 (COX‐2), which is highly expressed in various cancers. Research findings suggest that resveratrol (RSVL; 3,5,4′‐trihydroxy‐trans‐stilbene) demonstrates nonselective COX‐2 inhibition. We report herein that RSVL directly binds with COX‐2 and this binding is absolutely required for RSVL's inhibition of the ability of human colon adenocarcinoma HT‐29 cells to form colonies in soft agar. Binding of COX‐2 with RSVL was compared with two RSVL analogues, 3,3′,4′,5′,5‐pentahydroxy‐trans‐stilbene (RSVL‐2) or 3,4′,5‐trimethoxy‐trans‐stilbene (RSVL‐3). The results indicated that COX‐2 binds with RSVL‐2 more strongly than with RSVL, but does not bind with RSVL‐3. RSVL or RSVL‐2, but not RSVL‐3, inhibited COX‐2‐mediated PGE2 production in vitro and ex vivo. HT‐29 human colon adenocarcinoma cells express high levels of COX‐2 and either RSVL or RSVL‐2, but not RSVL‐3, suppressed anchorage independent growth of these cells in soft agar. RSVL or RSVL‐2 (not RSVL‐3) suppressed growth of COX‐2+/+ cells by 60% or 80%, respectively. Notably, cells deficient in COX‐2 were unresponsive to RSVL or RSVL‐2. These data suggest that the anticancer effects of RSVL or RSLV‐2 might be mediated directly through COX‐2. © 2008 Wiley‐Liss, Inc.
Deep brain pulse‐generator and lead‐extensions: Subjective sensations related to measured parameters
Authors: Sherif Camillo , Dorfer Christian , Kalteis Karin , Thun Caroline , Kaiser Iris , Gibson Daniel , Alesch François 
Published: March 2008

AbstractThis study analyzed subjective sensations caused by DBS pulse‐generator and lead‐extensions in relation with objectively measured parameters. In 50 patients implant‐related sensations were evaluated. The pulse‐generator mobility was video‐analyzed. Insufficient lead‐extension/pulse‐generator tolerability (72%/84%) was documented. Furthermore, 54% of the patients described movement impairments and 48% cosmetic deformity. High body mass index (BMI) was associated with low lead‐extension related pain (P < 0.001). High generator mobility resulted in high lead‐extension related pain (P < 0.001). Compared with lead‐extension type 7482, type 7495 showed less lead‐extension related pain (P = 0.0138), we suppose secondary to surgical tunneling instruments with a larger tip diameter. The lead‐extension path with one tissue tunnel for both lead‐extensions had 36% lead‐extension related pain versus 11% for the path with one single tunnel for each lead‐extension. Smaller pulse‐generators for better cosmetic results, surgical procedures using larger tunneling instruments and one single tunnel for each lead‐extension would provide better results forpatients with BMI <30. © 2008 Movement Disorder Society