bluuebunny/crossref_metadata_2025_split huggingface dataset:
Estimating probabilities of peptide database identifications to LC-FTICR-MS observations
Authors: Anderson Kevin K , Monroe Matthew E , Daly Don S 
Published: February 2006

Abstract

Background
The field of proteomics involves the characterization of the peptides and proteins expressed in a cell under specific conditions. Proteomics has made rapid advances in recent years following the sequencing of the genomes of an increasing number of organisms. A prominent technology for high throughput proteomics analysis is the use of liquid chromatography coupled to Fourier transform ion cyclotron resonance mass spectrometry (LC-FTICR-MS). Meaningful biological conclusions can best be made when the peptide identities returned by this technique are accompanied by measures of accuracy and confidence.

Methods
After a tryptically digested protein mixture is analyzed by LC-FTICR-MS, the observed masses and normalized elution times of the detected features are statistically matched to the theoretical masses and elution times of known peptides listed in a large database. The probability of matching is estimated for each peptide in the reference database using statistical classification methods assuming bivariate Gaussian probability distributions on the uncertainties in the masses and the normalized elution times.

Results
A database of 69,220 features from 32 LC-FTICR-MS analyses of a tryptically digested bovine serum albumin (BSA) sample was matched to a database populated with 97% false positive peptides. The percentage of high confidence identifications was found to be consistent with other database search procedures. BSA database peptides were identified with high confidence on average in 14.1 of the 32 analyses. False positives were identified on average in just 2.7 analyses.

Conclusion
Using a priori probabilities that contrast peptides from expected and unexpected proteins was shown to perform better in identifying target peptides than using equally likely a priori probabilities. This is because a large percentage of the target peptides were similar to unexpected peptides which were included to be false positives. The use of triplicate analyses with a "2 out of 3" reporting rule was shown to have excellent rejection of false positives.
The role of the peroxisome proliferator-activated receptor-α (PPAR-α) in the regulation of acute inflammation
Authors: Cuzzocrea Salvatore , Mazzon Emanuela , Di Paola Rosanna , Peli Angelo , Bonato Andrea , Britti Domenico , Genovese Tiziana , Muià Carmelo , Crisafulli Concetta , Caputi Achille P 
Published: February 2006

Abstract
The peroxisome proliferator-activated receptor-α (PPAR-α) is a member of the nuclear receptor superfamily of ligand-dependent transcription factors related to retinoid, steroid, and thyroid hormone receptors. The aim of the present study was to evaluate the role of the PPAR-α receptor on the development of acute inflammation. To address this question, we used two animal models of acute inflammation (carrageenan-induced paw edema and carrageenan-induced pleurisy). We report here that when compared with PPAR-α wild-type mice, PPAR-α knockout mice (PPAR-αKO) mice experienced a higher rate of the extent and severity when subjected to carrageenan injection in the paw edema model or to carrageenan administration in the pleurisy model. In particular, the absence of a functional PPAR-α gene in PPAR-αKO mice resulted in a significant augmentation of various inflammatory parameters (e.g., enhancement of paw edema, pleural exudate formation, mononuclear cell infiltration, and histological injury) in vivo. Furthermore, the absence of a functional PPAR-α gene enhanced the staining (immunohistochemistry) for FAS ligand in the paw and in the lung and the expression of tumor necrosis factor α and interleukin-1β in the lungs of carrageenan-treated mice. In conclusion, the increased inflammatory response observed in PPAR-αΚΟ mice strongly suggests that a PPAR-α pathway modulates the degree of acute inflammation in the mice.
Impairment of SHP-1 down-regulation in the lipid rafts of human neutrophils under GM-CSF stimulation contributes to their age-related, altered functions
Authors: Fortin Carl F , Larbi Anis , Lesur Olivier , Douziech Nadine , Fulop Tamas 
Published: February 2006

Abstract
It has been shown that the functions and the rescue from apoptosis by proinflammatory mediators of polymorphonuclear leukocytes (PMN) tend to diminish with aging. Here, we investigated the role of protein tyrosine phosphatases (PTP), especially Src homology domain-containing protein tyrosine phosphatase-1 (SHP-1), in the age-related, altered PMN functions under granulocyte macrophage-colony stimulating factor (GM-CSF) stimulation. The inhibition of PTP suggested a differential effect of GM-CSF on phosphatase activity in modulating PMN functions with aging. The down-regulation of phosphatase activity of immunopurified SHP-1 from lipid rafts of PMN of young donors was found significantly altered at 1 min of stimulation with aging. In young donors, SHP-1 is displaced from lipid rafts at 1 min of stimulation, whereas in the elderly, SHP-1 is constantly present. We assessed in PMN lipid rafts the phosphorylation of tyrosine and serine residues of SHP-1, which regulates its activity. We observed an alteration in the phosphorylation of tyrosine and serine residues of SHP-1 in PMN of elderly subjects, suggesting that GM-CSF was unable to inhibit SHP-1 activity by serine phosphorylation. GM-CSF activates Lyn rapidly, and we found alterations in its activation and translocation to the lipid rafts with aging. We also demonstrate that SHP-1 in the PMN of elderly is constantly recruited to Lyn, which cannot be relieved by GM-CSF. In contrast, in the young, the resting recruitment could be relieved by GM-CSF. Our results suggest an alteration of the SHP-1 modulation by GM-CSF in lipid rafts of PMN with aging. These alterations could contribute to the decreased GM-CSF effects on PMN.
Dendritic cell function in cytomegalovirus-infected patients with mononucleosis
Authors: Frascaroli Giada , Varani Stefania , Mastroianni Antonio , Britton Sven , Gibellini Davide , Rossini Giada , Landini Maria P , Söderberg-Nauclér Cecilia 
Published: February 2006

Abstract
Dendritic cells (DCs) are important target cells for human cytomegalovirus (HCMV) infection, and the virus has been shown to hamper the differentiation and maturation pathways of these cells in vitro. In the present study, we examined the function of monocyte-derived DCs obtained from immunocompetent individuals undergoing symptomatic HCMV infection in terms of immunophenotypic characteristics, pinocytosis, lymphocyte stimulation capacity, and cyto-chemokine secretion in comparison with DCs obtained from healthy controls. Immature and lipopolysaccharide (LPS)-stimulated DCs obtained from patients actively infected with HCMV expressed significantly lower levels of major histocompatibility complex (MHC) class II molecules. The inhibition of expression of MHC class II molecules by HCMV appeared to be functionally relevant, as mature DCs obtained from patients with HCMV mononucleosis were inefficient in stimulating proliferation of allogenic lymphocytes. Finally, the pattern of cyto-chemokines secreted by DCs obtained from patients with HCMV mononucleosis was characterized by a proinflammatory profile with an increased production of interleukin (IL)-1β, tumor necrosis factor α, CC chemokine ligand 2 (CCL2) and CCL3, and reduced secretion of IL-10 upon LPS stimulation. During symptomatic HCMV infection in the immunocompetent host, DCs exhibit an impaired immunophenotype and function. These effects may contribute to the viral-induced immunomodulation, which is often observed in HCMV-infected patients.
Polymorphonuclear neutrophils deliver activation signals and antigenic molecules to dendritic cells: a new link between leukocytes upstream of T lymphocytes
Authors: Megiovanni Anna Maria , Sanchez Françoise , Robledo-Sarmiento Macarena , Morel Céline , Gluckman Jean Claude , Boudaly Sarah 
Published: February 2006

Abstract
Polymorphonuclear neutrophils (PMNs) are rapidly recruited to tissues upon injury or infection. There, they can encounter local and/or recruited immature dendritic cells (iDCs), a colocalization that could promote at least transient interactions and mutually influence the two leukocyte populations. Using human live blood PMNs and monocyte-derived iDCs, we examined if these leukocytes actually interacted and whether this influenced DC function. Indeed, coculture with live but not apoptotic PMNs led to up-regulation of membrane CD40, CD86, and human leukocyte antigen (HLA)-DR on DCs. Whereas CD40 up-regulation was dependent on soluble factors released by PMNs, as determined in cultures conducted in different chambers, cell contact was necessary for CD86 and HLA-DR up-regulation, a process that was inhibited by anti-CD18 antibodies, indicating that CD18 ligation was required. We also found that via a cell contact-dependent mechanism, DCs acquired Candida albicans-derived antigens from live as well as from apoptotic PMNs and could thus elicit antigen-specific T lymphocyte responses. Altogether, our data demonstrate the occurrence of cross-talk between human PMNs and DCs and provide new insights into the immune processes occurring upstream of the interactions between DCs and T lymphocytes.
Inhibition of platelet-activating factor biosynthesis by adenosine and histamine in human neutrophils: involvement of cPLA2α and reversal by lyso-PAF
Authors: Flamand Nicolas , Lefebvre Julie , Lapointe Gabriel , Picard Serge , Lemieux Lise , Bourgoin Sylvain G , Borgeat Pierre 
Published: February 2006

Abstract
Leukotrienes (LT) and platelet-activating factor (PAF) are important lipid mediators of inflammation. We and others reported previously that autacoids such as adenosine, histamine, prostaglandin E2, and β-adrenergic agents inhibit LT biosynthesis in activated human polymorphonuclear leukocytes (PMN). In this study, we demonstrate that CGS-21680 (a selective agonist of the adenosine A2A receptor) and histamine also potently inhibit PAF biosynthesis in agonist [formyl Met-Leu-Phe (fMLP)]- and thapsigargin-activated human PMN. The observed inhibitions of PAF biosynthesis were reversed effectively by exogenous 1-O-alkyl-lyso-sn-glyceryl-3-phosphocholine (lyso-PAF), suggesting that these effects of CGS-21680 and histamine implicate the blockade of cytosolic phospholipase A2α (cPLA2α) activity and lyso-PAF release and that the acetyl-coenzyme A/lyso-PAF acetyl transferase is not inhibited by the autacoids. Accordingly, the cPLA2α inhibitor pyrrophenone completely blocked PAF formation, and lyso-PAF similarly prevented this effect of pyrrophenone. The inhibitory effects of CGS-21680 and histamine on PAF biosynthesis were prevented by the protein kinase A inhibitor H-89, supporting roles for the Gs-coupled receptors A2A and H2, respectively, and cyclic adenosine monophosphate in the inhibitory mechanism. The fMLP-induced phosphorylations of p38 and extracellular signal-regulated kinase 1/2 were not altered significantly by the CGS-21680, indicating that inhibition of these kinases is not involved in the inhibitory effect of the adenosine A2A receptor ligand on LT and PAF biosynthesis. These data further emphasize the multiple and potent inhibitory effects of adenosine and histamine on leukocyte functions, in particular, on the biosynthesis of two classes of important lipid mediators and their putative regulatory roles in immune processes in health and diseases.
Coupling of C3bi to IgG inhibits the tyrosine phosphorylation signaling cascade downstream Syk and reduces cytokine induction in monocytes
Authors: Trinidad Antonio García , De la Puerta María Luisa , Fernández Nieves , Bayón Yolanda , Crespo Mariano Sánchez , Alonso Andrés 
Published: February 2006

Abstract
The effect of coupling C3bi to immunoglobulin G (IgG) immune complexes (IC) on their ability to produce protein tyrosine phosphorylation and activation of the mitogen-activated protein kinase (MAPK) and the Akt/protein kinase B (PKB) routes was assessedin human monocytes. Cross-linking Fc receptors for IgG activated the protein tyrosine kinase Syk, phospholipases Cγ1 and Cγ2, the MAPK cascade, and the Akt/PKB route. Linkage of C3bi to the γ-chain of IgG produced a decrease of the protein bands displaying tyrosine phosphorylation, whereas the MAPK cascades and the Akt/PKB route remained almost unaffected. Zymosan particles, which because of their β-glucan content mimic the effect of fungi, produced a limited increase of tyrosine-phosphorylated protein bands, whereas treatment of zymosan under conditions adequate for C3bi coating increased its ability to induce protein tyrosine phosphorylation. Noteworthy, this was also observed under conditions where other components of serum might be bound by zymosan particles, for instance, serum IgG, thereby suggesting their potential involvement in Syk activation. The induction of cytokines showed a changing pattern consistent with the changes observed in the signaling pathways. IC induced monocyte chemoattractant protein-1 (MCP-1)/CC chemokine ligand 2 (CCL2), interleukin (IL)-1β, and eotaxin-2/CCL24, which were not observed with C3bi-coated IC. Zymosan induced the expression of tumor necrosis factor α (TNF-α), TNF-β, IL-10, IL-6, and MCP-2/CCL8, whereas the cytokine signature of C3bi-coated zymosan also included interferon-inducible protein 10/CXC chemokine ligand 10, platelet-derived growth factor-BB, and I-309/CCL1. Taken together, these findings indicate that C3bi targets the phagocytic cargo, and engagement or diversion of the Syk route determines the phagocyte response.
Hydrogenolysis-Isomerization-Reduction of Propargyl Acetate, and Regio- and Stereoselective Hydrogenation of Dienyl Ester for the Synthesis of 1β-Methylcarbapenem Precursor
Authors: Fujisawa Tamotsu , Hayakawa Ryuuichirou , Shimizu Makoto 
Published: March 2006

Abstract
A straightforward synthetic route of lβ-methylcarbapenem precursor is established by hydrogenolysis-isomerization-reduction process of propargyl acetate or by regio- and stereoselective hydrogenation process of dienyl ester with complete stereoselectivity.
Reactivities of Neutral and Cationic Organopalladium Complexes
Authors: Kayaki Yoshihito , Shimizu Isao , Yamamoto Akio 
Published: March 2006

Abstract
Novel, neutral and cationic monoorganopalladium complexes containing the methyl ligand as well as ethyl ligands having polar substituents have been prepared and their reactivities toward CO insertions have been compared. The results indicate that ready availability of CO coordination site in the complexes is the most important factor in determining the reactivities of the monoorganopalladium complexes toward CO insertion.
Generation of a Selenoaldehyde, a Selenoketone, and Telluroaldehydes by [3,3] Sigmatropic Rearrangement of Allyl Alkenyl Selenides and Tellurides
Authors: Shimada Kazuaki , Oikawa Seiji , Nakamura Hidenori , Takikawa Yuji 
Published: March 2006

Abstract
A selenoaldehyde, a selenoketone, and telluroaldehydes were generated by [3,3] sigmatropic rearrangement of allyl alkenyl selenides and tellurides, respectively, and were trapped with 2,3-dimethyl-1,3-butadiene to give the corresponding [4+2] cycloadducts.
A Highly Convenient, One-Pot Synthesis of 3-Bromo-1,5- and -1,7-Azulenequinones by Polybromination of Azulene
Authors: Nozoe Tetsuo , Wakabayashi Hidetsugu , Shindo Kimio , Kurihara Teruo , Ishikawa Sumio , Kageyama (the late) Masanori 
Published: March 2006

Abstract
A very convenient, one-pot synthesis (in ca. 80% yield) of 3-Bromo-1,5- and -1,7-azulenequinones which can be used as synthones has been developed by polybromination of azulenes. Zink dust reduction and reductive acetylation of these azulenequinones were studied, and possible pathways for the present synthesis are briefly discussed.
Activity of Alkaline and Alkaline-Earth Carbonates as Heterogeneous Catalysts for the Knoevenagel Condensation between Benzaldehyde and Malononitrile
Authors: Aramendia María Angeles , Borau Victoriano , Jimenez César , Marinas José María , Romero Francisco José 
Published: March 2006

Abstract
This paper reports the results obtained in the Knoevenagel condensation between benzaldehyde and malononitrile using various alkaline and alkaline-earth carbonates as catalysts. Within each carbonate series, the catalyst basicity increases with increasing ionic radius of the metal. Also, the catalytic activity increases with increase in the solid basicity.
Isolation and Characterization of Two Distinct Azurins from Alcaligenes xylosoxidans subsp. xylosoxidans NCIB11015 or GIFU1051
Authors: Yamaguchi Kazuya , Deligeer  , Nakamura Nobuhumi , Shidara Sohsuke , Iwasaki Hidekazu , Suzuki Shinnichiro 
Published: March 2006

Abstract
Two distinct azurins isolated from Alcaligenes xylosoxidans subsp. xylosoxidans NCIB11015 or GIFU1051 have been characterized by electronic absorption, circular dichroism (CD), and electronic paramagnetic resonance (EPR) spectroscopies. On the basis of CD spectra, two azurins from bacteria are clearly distinguishable.
Presence of Electrostatic Potential Wells in the Ionic Polymer Network
Authors: Gong Jianping , Osada Yoshihito 
Published: March 2006

Abstract
The electrostatic potential distribution of cross-linked polyelectrolyte gels has been numerically calculated on the base of Poisson-Boltzmann equation using a three dimensional network geometry. The simulational result revealed that besides potential energy valleys around the polymer chains, there should exist deep electrostatic potential energy wells at every cross-linking point.
Oxidation of Tetraarylselenophenes and Benzo[b]selenophene with m-Chloroperbenzoic Acid
Authors: Nakayama Juzo , Matsui Tomoki , Sato Noriko 
Published: March 2006

Abstract
Oxidation of tetraarylselenophenes with m-chloroperbenzoic acid produces cis-1,2-diaroyl-1,2-diarylethylenes and SeO2 as the principal product, while the oxidation of benzo[b]selenophene affords benzo[b]selenophene 1-oxide.
The Development of a Program Visualizing Results of Vibrational Analysis Calculation Using ab initio Molecular Orbital Method
Authors: Tsutsui Yuko , Wasada Hiroaki 
Published: March 2006

Abstract
We developed a computer program MOLCAT to visualize results of vibrational analysis calculation. This program can treat Z-matrix used in ab initio molecular orbital calculation, and shows the vibrational mode as arrows with the molecular structure. We applied this program to show transition vectors of the intramolecular inversion of ammonia and the water exchange reaction of hexaaquacalcium(II). We are preparing to distribute MOLCAT as a free software.
Synthesis and Structure of a New Tripodal Polypyridine Copper(II) Complex That Enables to Recognize a Small Molecule
Authors: Harata Manabu , Jitsukawa Koichiro , Masuda Hideki , Einaga Hisahiko 
Published: March 2006

Abstract
With a view to constructing an artificial metalloenzyme model complex which can recognize and capture a small molecule, a new tripodal ligand, tris(6-pivaloylamino-2-pyridylmethyl)amine, and its mononuclear copper(II) complex has been synthesized, and they were characterized by 1H-NMR and positive-ion FAB mass spectra, cyclic voltammetry and X-ray structure analysis.
Preparation and Structure of 2,3-Dichloro-1,4-bis(2,4,6-tri-t-butylphenyl)-1,4-diphospha-1,3-butadiene
Authors: Ito Shigekazu , Toyota Kozo , Yoshifuji Masaaki 
Published: March 2006

Abstract
A sterically protected 1,4-diphospha-1,3-butadiene was prepared from the copper-mediated coupling reaction of 2,2-dichloro-1-(2,4,6-tri-t-butylphenyl)-1-phosphaethene. The X-ray crystallographic analysis shows that the molecule has a center of symmetry and that each of the bulky phenyl groups tilts almost perpendicularly to the diphosphabutadiene system serving as a good protecting group.
O2-Transport Albumin: A New Hybrid-Haemoprotein Incorporating Tetraphenylporphinatoiron(II) Derivative
Authors: Komatsu Teruyuki , Ando Katsutoshi , Kawai Noriyuki , Nishide Hiroyuki , Tsuchida Eishun 
Published: March 2006

Abstract
2-[8-{N-(2-methylimidazolyl)}octanoyloxymethyl]-5,10,15,20-tetrakis(α,α,α,α-o-pivalamido)phenylporphinatoiron(II) is incorporated into the human serum albumin, which reversibly forms a stable O2-adduct under physiological conditions (in aqueous medium, pH 7.4, 37 °C) similar to haemoglobin.
Molecular Recognition of Horse Heart Apomyoglobin to Monopropionate Hemin: Thermodynamic Determination of Two Orientational Isomers by 1H NMR Spectra
Authors: Hayashi Takashi , Hitomi Yutaka , Suzuki Akihiro , Takimura Tetsuo , Ogoshi Hisanobu 
Published: March 2006

Abstract
Four synthetic hemins, 1,3,5,8-tetramethyl-2,4-diethyl-6,7-dipropionate hemin (1), 1,2,3,4-tetraethyl-5,6,8-trimethyl-7-propionate hemin (2), 1,3,5,6,8-pentamethyl-2,4-diethyl-7-propionate hemin (3) and 1,3,5,7,8-pentamethyl-2,4-diethyl-6-propionate hemin (4) were prepared and incorporated into apomyoglobin to clarify hydrophilic interaction of the hemin propionate with particular polar amino acid residues. Favorable orientation of hemin in protein is interpreted by thermodynamic study using 1H NMR measurement.
Preparation and Characterization of Di-μ-oxo Dimanganese(IV) Complexes with Bidentate Schiff Bases, N-Alkyl-salicylideneamine
Authors: Torayama Hitoshi , Asada Hideyuki , Fujiwara Manabu , Matsushita Takayuki 
Published: March 2006

Abstract
Novel di-μ-oxo dimanganese(IV) complexes, [MnIV(N-R-sal)2(μ-O)]2, with bidentate Schiff base ligands, N-alkyl-salicylideneamine, N-R-salH (R = n-C3H7 (Pr), n-C4H9 (Bu), n-C6H13 (Hx), n-C8H17 (Oct), n-C12H25 (Dod), or n-C18H37 (Octd)), have been prepared and characterized by spectroscopies, magnetic susceptibilities, thermal analysis and X-ray crystallography.
Ruthenium-Catalyzed Addition of Aromatic Esters at the ortho C–H Bonds to Olefins
Authors: Sonoda Motohiro , Kakiuchi Fumitoshi , Kamatani Asayuki , Chatani Naoto , Murai Shinji 
Published: March 2006

Abstract
A ruthenium complex, Ru(H)2(CO)(PPh3)3, can catalyze the addition of aromatic and heteroaromatic esters at the ortho carbon-hydrogen bonds to olefinic double bonds. While un-substituted alkyl benzoate did not react, those substituted with CF3 or F underwent smooth catalytic addition. A heteroaromatic ester and a benzo-δ-lactone also reacted.
New Electrochemical Preparation of Reactive Zinc with a Large Surface Area
Authors: Tokuda Masao , Kurono Nobuhito , Mimura Nobuo 
Published: March 2006

Abstract
Reactive zinc was readily prepared by electrolysis of a DMF solution containing 0.1 M Et4NClO4 using a platinum cathode and a zinc anode. Characterization of the zinc metal showed that it was an aggregation of very fine, crystalline zinc particles with a specific surface area of 24 m2/g, which is 100 times larger than that of commercial zinc metals. Preparation of zinc with a much larger surface area of 56 m2/g could be achieved by electrolysis of the solution at a lower current density.
Asymmetric Allylation of Aromatic Aldehydes Using Chiral Allylic Tin Reagents
Authors: Nishida Minoru , Tozawa Takashi , Yamada Koji , Mukaiyama Teruaki 
Published: March 2006

Abstract
Chiral allylating reagents, readily generated in situ from 2λ2-1,3,2-benzodioxastannole [SnII(O2C6H4)], allyl halides, chiral dialkyl tartrates and 1,8-diazabicyclo[5.4.0]-7-undecene (DBU) smoothly react with aromatic aldehydes at −78 °C in the presence of a catalytic amount of copper salts to afford the corresponding homoallylic alcohols in high yields with high enantioselectivities.
The Effect of Pressure on the Surface Structure of MgO/BaCO3 Catalyst for Oxidative Coupling of Methane
Authors: Liu Yu , Yu Changchun , Liu Xuxia , Zhang Bing , Shen Shikong 
Published: March 2006

Abstract
The effect of pressure on oxidative coupling of methane (OCM) over MgO/BaCO3 catalyst was studied at the range of 0.1∼1.1 MPa at 1053 K. Deactivation of the MgO/BaCO3 catalyst at elevated pressure was attributed to the migration of BaCO3 from bulk to the surface of the catalyst.