bluuebunny/crossref_metadata_2025_split huggingface dataset:
Computational investigation of kinetics of cross‐linking reactions in proteins: Importance in structure prediction
Authors: Bandyopadhyay Pradipta , Kuntz Irwin D. 
Published: September 2008

AbstractThe determination of protein structure using distance constraints is a new and promising field of study. One implementation involves attaching residues of a protein using a cross‐linking agent, followed by protease digestion, analysis of the resulting peptides by mass spectroscopy, and finally sequence threading to detect the protein folds. In the present work, we carry out computational modeling of the kinetics of cross‐linking reactions in proteins using the master equation approach. The rate constants of the cross‐linking reactions are estimated using the pKas and the solvent‐accessible surface areas of the residues involved. This model is tested with fibroblast growth factor (FGF) and cytochrome C. It is consistent with the initial experimental rate data for individual lysine residues for cytochrome C. Our model captures all observed cross‐links for FGF and almost 90% of the observed cross‐links for cytochrome C, although it also predicts cross‐links that were not observed experimentally (false positives). However, the analysis of the false positive results is complicated by the fact that experimental detection of cross‐links can be difficult and may depend on specific experimental conditions such as pH, ionic strength. Receiver operator characteristic plots showed that our model does a good job in predicting the observed cross‐links. Molecular dynamics simulations showed that for cytochrome C, in general, the two lysines come closer for the observed cross‐links as compared to the false positive ones. For FGF, no such clear pattern exists. The kinetic model and MD simulation can be used to study proposed cross‐linking protocols. © 2008 Wiley Periodicals, Inc. Biopolymers 91: 68–77, 2009.This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com
Mitigating climate change – how do corporate strategies differ?
Authors: Weinhofer Georg , Hoffmann Volker H. 
Published: September 2008

AbstractMany companies are facing increasing pressure by governments, shareholders and other stakeholders to reduce their CO2 emissions in order to mitigate climate change. The importance of managing CO2 emissions and crafting adequate CO2 strategies has increased for those companies affected. We present a framework that conceptualizes a company's CO2 strategy as the focus on one or a combination of several strategic objectives: CO2 compensation, CO2 reduction and carbon independence. In order to investigate the CO2 strategies of a worldwide sample of 91 electricity producers we perform a content analysis of their answers to the Carbon Disclosure Project (CDP). We demonstrate the measures the companies take to manage their emissions, the CO2 strategies they adopt and antecedents that influence these strategies. We find that half of the companies take parallel emission management measures that aim at all three strategic objectives, while the other half pursue selected objectives only. We also find that companies with different CO2 strategies significantly differ in terms of regional affiliation, company size and absolute amount of CO2 emissions, while we could not identify a significant difference in relative CO2 emissions. Copyright © 2008 John Wiley & Sons, Ltd and ERP Environment.
DNA with Branched Internal Side Chains: Synthesis of 5‐Tripropargylamine‐dU and Conjugation by an Azide‐Alkyne Double Click Reaction
Authors: Sirivolu Venkata Ramana , Chittepu Padmaja , Seela Frank 
Published: September 2008

Abstract5‐Tripropargylamine‐2′‐deoxyuridine (1 a) containing two terminal triple bonds was synthesized by a Pd‐assisted Sonogashira cross‐coupling reaction and was subsequently converted into the corresponding phosphoramidite building block (9) and employed in solid‐phase oligonucleotide synthesis. Tm experiments demonstrate that the presence of covalently attached branched tripropargylamine residues has a positive effect on the base pair stability. The two terminal CC bonds of modified DNA were functionalized by means of CuI‐mediated 1,3‐dipolar cycloaddition reactions (click chemistry) with azides such as 3‐azido‐7‐hydroxycoumarin or 3′‐azido‐3′‐deoxythymidine (AZT) both in solution and on solid support. In particular, with the nonfluorescent 3‐azido‐7‐hydroxycoumarin a strongly fluorescent oligonucleotide bis‐dye conjugate was generated. For comparison, the N(3)‐propargylated 2′‐deoxyuridine 2 was prepared from 2′‐deoxyuridine and propargyl bromide and incorporated into DNA. The two terminal triple bonds of 1 a allow the simultaneous post‐modification of DNA by two reporter molecules and can be applied to almost any azido derivatives (oligonucleotides, proteins, polysaccharides etc.) including those forming dendrimeric side chains.
Tomato CYP74C3 is a Multifunctional Enzyme not only Synthesizing Allene Oxide but also Catalyzing its Hydrolysis and Cyclization
Authors: Grechkin Alexander N. , Mukhtarova Lucia S. , Latypova Larisa R. , Gogolev Yuri , Toporkova Yana Y. , Hamberg Mats 
Published: September 2008

AbstractThe mechanism of the recombinant tomato allene oxide synthase (LeAOS3, CYP74C3) was studied. Incubations of linoleic acid (9S)‐hydroperoxide with dilute suspensions of LeAOS3 (10–20 s, 0 °C) yield mostly the expected allene oxide (12Z)‐9,10‐epoxy‐10,12‐octadecadienoic acid (9,10‐EOD), which was detected as its methanol‐trapping product. In contrast, the relative yield of 9,10‐EOD progressively decreased when the incubations were performed with fourfold, tenfold, or 80‐fold larger amounts of LeAOS3, while α‐ketol and the cyclopentenone rac‐cis‐10‐oxo‐11‐phytoenoic acid (10‐oxo‐PEA) became the predominant products. Both the α‐ketol and 10‐oxo‐PEA were also produced when LeAOS3 was exposed to preformed 9,10‐EOD, which was generated by maize allene oxide synthase (CYP74A). LeAOS3 also converted linoleic acid (13S)‐hydroperoxide into the corresponding allene oxide, but with about tenfold lower yield of cyclopentenone. The results indicate that in contrast to the ordinary allene oxide synthases (CYP74A subfamily), LeAOS3 (CYP74C subfamily) is a multifunctional enzyme, catalyzing not only the synthesis, but also the hydrolysis and cyclization of allene oxide.
Nucleation and Growth of BaFxCl2−x Nanorods
Authors: Xie Ting , Li Shuai , Wang Wenbei , Peng Qing , Li Yadong 
Published: September 2008

AbstractDifferent ratios and sizes of Ba2F3Cl (BaFxCl2−x, x=1.5) nanorods and nanowires and orthorhombic BaF2 (BaFxCl2−x, x=2) nanorods were prepared by using a liquid–solid–solution approach at 160∼180 °C. The processes and results of the experiments conducted to prepare monodisperse Ba2F3Cl nanorods and nanowires showed that the specific surface area increased as the initial concentrations were multiplied. Based on this fact, a mechanism for the nucleation and growth processes of these nanocrystals that have a variety of enlarged sizes was substantiated in view of the surface chemical thermodynamics (SCT). In this SCT mechanism, the specific surface energy takes into account both the surfactant oleic acid and the nanocrystal surface, and is dominated by the chemical potential of the adsorbate.
Zipped‐Up Chain‐Type Coordination Polymers: Unsymmetrical Amide‐Containing Ligands Inducing β‐Sheet or Helical Structures
Authors: Uemura Kazuhiro , Kumamoto Yuki , Kitagawa Susumu 
Published: September 2008

AbstractThe crystal structures of thirteen AgI coordination polymers involving py‐CONH‐(CH2)n‐py (py=pyridine; n=0, 1) derivatives were determined by means of single‐crystal X‐ray analyses. All of the compounds form one‐dimensional chains composed of AgI atoms and bridging ligands with formulas {[Ag(py‐CONH‐(CH2)n‐py)][X]}n (X=PF6−, ClO4−, BF4−, and NO3− with solvent molecules). The unsymmetrical coordination environments around AgI atoms induce direction in the chains, that is, ‐[NH‐(CH2)n‐py‐Ag‐py‐CO]‐, which resembles the alignment of amino acid chains in proteins. In compounds {[Ag(4‐pia)][X]}n (1⊃X; 4‐pia=N‐(4‐pyridyl)isonicotinamide; X=PF6−, ClO4−, BF4−, and NO3−), {[Ag(4‐pmia)][X]}n (2⊃X; 4‐pmia=N‐(pyridin‐4‐ylmethyl)isonicotinamide; X=PF6−, ClO4−⋅H2O, and NO3−⋅H2O), and {[Ag(3‐pmia)][X]}n (3⊃X; 3‐pmia=N‐(pyridin‐3‐ylmethyl)isonicotinamide; X=PF6−, ClO4−, BF4−, and NO3−⋅H2O), each chain is aligned parallel to neighboring chains, but adjacent chains run in the opposite direction. Particularly in {[Ag(3‐pmia)][PF6]}n (3⊃PF6−), {[Ag(3‐pmia)][ClO4]}n (3⊃ClO4−), and {[Ag(3‐pmia)][BF4]}n (3⊃BF4−), amide moieties of 3‐pmia ligands are complementarily hydrogen bonded to amide moieties in neighboring chains, as in the β‐sheet motif in proteins. On the other hand, in {[Ag(4‐pmna)][PF6]⋅MeOH}n (4‐pmna=N‐(pyridin‐4‐ylmethyl)nicotinamide), all chains in the crystal form left‐handed (4 a⊃PF6−⋅MeOH) and right‐handed (4 b⊃PF6−⋅MeOH) helical structures with a helical pitch of 28 Å. Heterogeneous anion exchanges proceed reversibly in 2, but not in 3, which provides information about the thermal stabilities of the crystals.
Expanding Sapphyrin: Towards Selective Phosphate Binding
Authors: Katayev Evgeny A. , Boev Nikolay V. , Myshkovskaya Ekaterina , Khrustalev Victor N. , Ustynyuk Yu. A. 
Published: September 2008

AbstractThe anion‐templated syntheses and binding properties of novel macrocyclic oligopyrrole receptors in which pyrrole rings are linked through amide or imine bonds are described. The efficient synthesis was accomplished by anion‐templated [1+1] Schiff‐base condensation and acylation macrocyclization reactions. Free receptors and their host–guest complexes with hydrochloric acid, acetic acid, tetrabutylammonium chloride, and hydrogen sulfate were analyzed by single‐crystal X‐ray diffraction analysis. Stability constants with different tetrabutylammonium salts of inorganic acids were determined by standard 1H NMR and UV/Vis titration techniques in [D6]DMSO/0.5 % water solution. According to the titration data, receptors containing three pyrrole rings (10 and 12) exhibit high affinity (log Ka=5–7) for bifluoride, acetate, and dihydrogen phosphate, and interact weakly with chloride and hydrogen sulfate. The amido‐bipyrrole receptors 11 and 13 with four pyrrole rings exhibit 104‐ and 102‐fold selectivity for dihydrogen phosphate, respectively, as inferred from competitive titrations in the presence of tetrabutylammonium acetate.
Electrochemical Functionalization of Carbon Surfaces by Aromatic Azide or Alkyne Molecules: A Versatile Platform for Click Chemistry
Authors: Evrard David , Lambert François , Policar Clotilde , Balland Véronique , Limoges Benoît 
Published: September 2008

AbstractThe electrochemical reduction of phenylazide or phenylacetylene diazonium salts leads to the grafting of azido or ethynyl groups onto the surface of carbon electrodes. In the presence of copper(I) catalyst, these azide‐ or alkyne‐modified surfaces react efficiently and rapidly with compounds bearing an acetylene or azide function, thus forming a covalent 1,2,3‐triazole linkage by means of click chemistry. This was illustrated with the surface coupling of ferrocenes functionalized with an ethynyl or azido group and the biomolecule biotin terminated by an acetylene group.
Photo‐, Solvent‐, and Ion‐Controlled Multichromism of Imidazolium‐Substituted Diarylethenes
Authors: Nakashima Takuya , Miyamura Kentaro , Sakai Toshiyuki , Kawai Tsuyoshi 
Published: September 2008

AbstractSeeing red: Imidazolium‐substituted diarylethenes show solvent‐ and ion‐controlled chromisms in addition to reversible photochromic reactions. The shift of equilibrium between two closed‐ring isomers with different π‐conjugation length by interaction with nucleophilic species is responsible for the multichromic property (see scheme).magnified imageCationic diarylethenes with an imidazolium ring are synthesized for the first time. The imidazolium cationic moiety is connected directly to the ethene unit as one of the aryl units that take part in the photoinduced pericyclization reaction. The imidazolium‐substituted diarylethenes undergo reversible photochromic reactions in a variety of organic media, including ionic liquids, even though they have a delocalized cationic charge in one of the five‐membered aromatic rings. The closed‐ring isomer shows solvatochromism depending on the solvent donor numbers. Addition of some tetraalkylammonium salts, such as tetrabutyl ammonium nitrate, into the colored organic solution of diarylethene also causes a color change, indicating its ionochromic property. These solvato‐ and ionochromic properties are considered in connection with the shift of chemical equilibrium between the closed‐ring isomers, one with an extended π‐conjugation system and one with limited π‐conjugation due to the strong interaction with solvent molecules and anions with high donor number.
Self‐Assembly of Oligo(para‐phenylenevinylene)s through Arene—Perfluoroarene Interactions: π Gels with Longitudinally Controlled Fiber Growth and Supramolecular Exciplex‐Mediated Enhanced Emission
Authors: Babu Sukumaran S. , Praveen Vakayil K. , Prasanthkumar Seelam , Ajayaghosh Ayyappanpillai 
Published: September 2008

AbstractThe arene–perfluoroarene (ArH–ArF) interaction, which has been extensively studied in the field of solid‐state chemistry, is exploited in the hierarchical self‐assembly of oligo(para‐phenylenevinylene)s (OPVs) with controlled longitudinal fiber growth that leads to gelation. The size of the self‐assembled fibers of a pentafluorophenyl‐functionalized OPV 5 could be controlled through C‐F⋅⋅⋅HC hydrogen bonding and π stacking. The ability of fluoroaromatic compounds to form excited‐state complexes with aromatic amines has been utilized to form a supramolecular exciplex, exclusively in the gel state, that exhibits enhanced emission. Thus, the commonly encountered fluorescence quenching during the self‐assembly of OPVs could be considerably prevented by exciplex formation with N,N‐dimethylaniline (DMA), which only occurred for the fluorinated OPV and not for the non‐fluorinated analogue 4. In the former case, a threefold enhancement in the emission intensity could be observed in the gel state, whereas no change in emission occurred in solution. Thus, the major limitations of spontaneous fiber growth and fluorescence self‐quenching encountered in the self‐assembly of OPVs could be controlled to a great extent by using the versatile ArH–ArF interaction.
Clinical Implications of Elevated Serum Interleukin‐6, Soluble CD40 Ligand, Metalloproteinase‐9, and Tissue Inhibitor of Metalloproteinase‐1 in Patients with Acute ST‐segment Elevation Myocardial Infarction
Authors: Tan Jing , Hua Qi , Gao Jing , Fan Zhen Xing 
Published: September 2008

AbstractBackgroundAtherosclerosis is widely accepted as a chronic inflammatory disease. Research paid much attention to sensitive specific serum biomarkers for vulnerable plaques. The markers not only serve as diagnostic tools for the identification of patients with acute coronary syndrome (ACS), but also help us to identify high‐risk patients. However, the existing data are limited and have been conflicting.HypothesisCirculating interleukin‐6 (IL‐6), soluble CD40 ligand (sCD40L), metalloproteinase‐9 (MMP‐9), and tissue inhibitor of metalloproteinase‐1 (TIMP‐1) might correlate with the onset and the cardiac mortality of patients with ST‐segment elevation myocardial infarction (STEMI).MethodsSerum levels of IL‐6, sCD40L, MMP‐9, and TIMP‐1 were measured by sandwich enzyme‐linked immunosorbent assay (ELISA) in 263 patients with STEMI and 262 age‐ and gender‐matched control subjects without coronary artery disease (CAD). The patients with STEMI were then followed prospectively for 24 mo for the occurrence of cardiac mortality.ResultsCompared with the control subjects, patients with STEMI exhibited higher levels of IL‐6 (p < 0.001), sCD40L (p < 0.001), MMP‐9 (p < 0.001), TIMP‐1 (p = 0.045), and MMP‐9/TIMP‐1 ratio (p = 0.007). Significant and positive correlations between MMP‐9 and TIMP‐1 (r = 0.610, p≤0.001]), IL‐6 and creatine kinase (CK) (r = 0.159, p = 0.022), and IL‐6 and Troponin‐I (TnI) (r = 0.141, p = 0.042) were observed by Spearman's correlations analysis. Logistic regression analysis revealed that IL‐6 significantly and independently correlated with the occurrence of STEMI, and IL‐6 was an independent predictor for cardiac mortality during a 24‐mo follow‐up in patients with STEMI.ConclusionThe present study indicates that elevated admission level of IL‐6, but not of sCD40L, MMP‐9, or TIMP‐1, might indicate the onset of STEMI, and could provide prognostic value for future cardiac mortality within 2 y in patients with STEMI. Copyright © 2008 Wiley Periodicals, Inc.
Myocardial and Aortic Stiffening in the Early Course of Primary Aldosteronism
Authors: Tsioufis Costas , Tsiachris Dimitrios , Dimitriadis Kyriakos , Stougiannos Pavlos , Missovoulos Platonas , Kakkavas Apostolis , Stefanadis Christodoulos , Kallikazaros Ioannis 
Published: September 2008

AbstractBackgroundPrimary aldosteronism (PA) has been experimentally and clinically linked to myocardial and vascular fibrosis, and it has been further associated with left ventricular (LV) structural adaptations.HypothesisFunctional cardiovascular adaptations in hypertensive patients with PA precede structural alterations in the early stages of the disease.MethodsWe studied 17 hypertensive subjects with a recent diagnosis of PA (10 male patients, aged approximately 55 y, with office blood pressure [BP] of 137/88 mm Hg), and 30 essential hypertensives matched for age, sex, office BP levels, treatment status, and LV mass index (LVMI). Apart from standard 2‐Dimensional (2‐D) and conventional Doppler parameters, tissue Doppler imaging (TDI) methodology was used to assess LV diastolic function; averaging early and late diastolic mitral annular peak velocities (Emav/, Amav, Emav/Amav ratio) from 4 separate sites of measurement (septal, lateral, anterior, and inferior walls). Aortic stiffness was evaluated by means of carotid‐femoral pulse wave velocity (cf‐PWV) measurements.ResultsAlthough transmitral E/A ratio was similar in both groups (0.95 ± 0.26 versus 0.98 ± 0.24, ± p 0.66), hypertensive subjects with PA compared with essential hypertensives are characterized by significantly higher relative wall thickness (0.50 ± 0.07 versus 0.41 ± 0.06, p ≤ 0.001), decreased values of Emav (7 ± 1.7 versus 8.1 ± 1.8 cm/s, p= 0.048), and Emav/Amav ratio (0.63 ± 0.16 versus 0.77 ± 0.17, p = 0.015). The higher PWV in the PA population failed to reach statistical significance (8.5 ± 1.6 versus 7.9 ± 0.9 msec, p = 0.19).ConclusionOur study demonstrates altered LV geometry and TDI‐revealed diastolic dysfunction in hypertensives with PA compared with demographically‐ and LVMI‐matched essential hypertensives. Furthermore, the increased aortic stiffening in PA patients failed to reach statistical significance. Copyright © 2008 Wiley Periodicals, Inc.
Endogenous B‐type Natriuretic Peptide: A Limb of the Regulatory Response to Acutely Decompensated Heart Failure
Authors: Hobbs Robert E. , Mills Roger M. 
Published: September 2008

AbstractAcutely decompensated heart failure (ADHF) represents an episodic failure of cardiorenal homeostasis that may resolve with upregulation of natriuretic peptides, bradykinin, and certain prostacyclins. B‐type natriuretic peptide (BNP) has multiple favorable effects, including vasodilation, diuresis, natriuresis, and inhibition of vascular endothelial proliferation and cardiac fibrosis. By antagonizing the effects of activation of the renin‐angiotensin‐aldosterone system (RAAS) and the sympathetic nervous system in volume overload, the endogenous BNP response may help rescue patients from episodic ADHF. Although knowledge of BNP physiology is expanding, we still have limited understanding of the heterogeneity of proBNP‐derived molecules, including active 32 amino acid BNP and less active junk BNP forms. Emerging evidence suggests that in ADHF, the endogenous BNP response is overwhelmed by neurohormonal activation. This relative BNP deficiency may also be accompanied by physiologic resistance to BNP. Additionally, abnormalities of BNP production may result in a lower proportion of active BNP relative to less active forms that may also be detected by point‐of‐care tests. Improved detection of the various BNP species may clarify these concepts and facilitate improved clinical management of ADHF. Copyright © 2008 Wiley Periodicals, Inc.
Reassessing the Cardiovascular Risks and Benefits of Thiazolidinediones
Authors: Zinn Andrew , Felson Sabrina , Fisher Edward , Schwartzbard Arthur 
Published: September 2008

AbstractThis article is designed for the general cardiologist, endocrinologist, and internist caring for patients with diabetes and coronary artery disease. Despite the burden of coronary disease in diabetics, little is known about the impact of commonly used oral hypoglycemic agents on cardiovascular outcomes. As the untoward effects of insulin resistance (IR) are increasingly recognized, there is interest in targeting this defect. Insulin resistance contributes to dyslipidemia, hypertension, inflammation, hypercoagulability, and endothelial dysfunction. The aggregate impact of this process is progression of systemic atherosclerosis and an increased risk of adverse cardiovascular outcomes. As such, much attention has been paid to the peroxisome‐proliferator‐activated receptor gamma (PPARg) agonists rosiglitazone and pioglitazone (thiazolidinediones [TZDs]). Many studies have demonstrated a beneficial effect on the atherosclerotic process; specifically, these agents have been shown to reduce markers of inflammation, retard progression of carotid intimal thickness, prevent restenosis after coronary stenting, and prevent cardiovascular death and myocardial infarction in 1 large trial. Such benefits come at the risk of fluid retention and heart failure (HF) exacerbation, and the net effect on plasma lipids is still poorly understood. Thus, the aggregate risk‐benefit ratio is poorly defined. A recent meta‐analysis has raised significant concerns regarding the overall cardiovascular safety of 1 particular PPARg agonist (rosiglitazone), prompting international debate and regulatory changes. This review scrutinizes the clinical evidence regarding the cardiovascular risks and benefits of PPARg agonists. Future studies of PPARg agonists, and other emerging drugs that treat IR and diabetes, must be designed to look at cardiovascular outcomes. Copyright © 2008 Wiley Periodicals, Inc.
Blood Pressure Measurement: Sitting and Standing?
Authors: Richard Conti C. 
Published: September 2008

AbstractPrior to discussing some thoughts about positional changes in blood pressure, I'd like to comment on the me‐ asurement of blood pressure.It is rare for a medical student, a resident‐in‐training, a cardiovascular fellow‐in‐training, or even a practicing or academic cardiologist to take the patient's blood pressure. I would even go so far as to say that it is uncommon for a registered nurse to measure blood pressure. Copyright © 2008 Wiley Periodicals, Inc.