bluuebunny/crossref_metadata_2025_split huggingface dataset:
Les belles lettres : écriture et ornement sur une œnochoé de Charinos
Authors: Lissarrague François 
Published: September 2009

Les belles lettres : écriture et ornement sur une oenochoé de Charinos (pp. 123-133)
Le rapport entre ornement, écriture et représentation est particulièrement étroit sur une œnochoé signée du potier Charinos. La connivence entre le feuillage et les lettres s'inscrit dans un ensemble d'expérimentations graphiques et plastiques (fond blanc, décor en silhouette, absence de figure humaine) qui mettent en valeur la beauté d'une femme - Xénodoké - et la qualité du vase lui-même. Un tel objet appartient à une petite série de vases, rares mais révélateurs des possibilités esthétiques de l'écriture, quand elle fait image.
Une femme, un homme, autour d'un pithos
Authors: Noël Daniel 
Published: September 2009

Une femme, un homme, autour d'un pithos (pp. 346-381)
Dix lécythes représentent la confiscation héracléenne du vin en Centaurie selon une même scénographie. Héraclès, un Centaure, une femme et un homme, s'affairent autour d'un pithos. A la Pithoigia, les jarres étaient descellées et le vin nouveau devenait consommable par l'enchaînement de rites qui unissaient Dionysos, le vin et la cité. L'ouverture du pithos de vin éveille des rapprochements avec la fête du même nom à Athènes.
Les imagiers explorèrent la Centaurie comme un lieu exceptionnel pour questionner à nouveau le vin. Ici, comme en cité, l'assise communautaire repose sur un certain ordre du vin. La Centaurie serait un détour édifiant sur la place du vin en cité et le rapport à l'autre.
Omero, Odisseo e Luciano : una lettura di Storia vera, I, 3
Authors: Saraceno Camilla 
Published: September 2009

Omero, Odisseo e Lucia.no: una lettura di Storia vera, I, 3 (pp. 401-416)
Le renvoi à l'Ulysse d'Homère comme αρχηγός et διδάσκαλος de tous les menteurs dans le «prologue» de l'Histoire vraie (I, 3), semble être plus qu'un simple rappel à la tradition littéraire; il laisse entrevoir le rapport ambigu, admiratif et critique en même temps, qui lie Lucien à Homère. L'admiration pour le poète épique était naturelle; la critique naissait de la polémique, chère à Lucien, contre le mensonge (qu'il repérait surtout chez les poètes). L'allusion à la section des Apologoi de l'Odyssée révèle cette polémique et détermine aussi un genre de récit critique et parodique, le récit de voyage fantastique; en même temps elle sert à justifier la présence du ψεϋδος dans la prose de Lucien. Homère devient ainsi inspirateur et objet de parodie à la fois.
Ancient viewing and modern art history
Authors: Elsner Jas 
Published: September 2009

Ancient Viewing and Modem Art History (pp. 4 17-437)
Le présent article examine s'il existe, chez les écrivains grecs du monde romain, une connaissance historique de l'art qui s'intéresse à la définition du style artistique. Il porte en particulier sur Pausanias, pour les notions de «mains» individuelles et pour quelques cas d'identifications d'artistes; et sur Lucien, pour les idées de styles ethnique et/ou régional. Ces deux théories du style sont très répandues dans l'histoire moderne de l'art, et le présent article tente de comparer la pratique moderne avec ces antécédents greco-romains.
Abinitioand Semiempirical Methods
Authors: Gorelsky Serge I. 
Published: September 2009

AbstractAb initio and semiempirical methods play a very important role in modern computational chemistry. The main advantage of semiempirical methods is a substantial reduction in the required computation time and, consequently, an increase in ability to execute calculations for large molecules. The disadvantages are the loss of the variational principle (one can obtain a total energy that is below the true total energy), the limited applicability (methods can only be applied to molecules containing elements that have been parameterized), and the danger of spurious results (especially for molecular systems that are different from those used for parameterizations). On the other hand, high‐level ab initio techniques enable researchers to obtain very accurate results and act as a reference to lower‐accuracy methods. These ab initio methods play an important role for calculations of small molecular systems and progress is being made to extend the area of application of such methods to bigger systems.
Computational Studies: Proton/Water Coupling to Metals in Biological Reaction Mechanisms
Authors: Bu Y. , Cukier R. I. 
Published: September 2009

Abstract
Metalloenzymes promote a wide variety of reaction chemistry with the use of protons and water, and associated ligands and protein residues. The charges/oxidation states of the metals and many charged and/or highly polar residues and ligands produce strong effects on acid‐base‐driven chemistry. Computational approaches to metalloenzyme mechanisms require a compromise between accuracy (use of high‐level quantum chemical methods) and the ability to handle many atoms (use of force field methods). Methods that divide the system into a part that is treated accurately and a part treated at a lower level require careful attention toward the chemistry of the specific system. In this article, we outline a number of our recent approaches to some enzymatic reactions where metals, protons, and water are intimately coupled. Three metalloenzymes, cytochrome c oxidase, cytosine deaminase, and calcium ATPase (a calcium pump), are discussed using methods that divide an enzyme into a reaction zone treated at a high level and the remainder treated at a lower level.
Reaction Coordinate of Pyranopterin Molybdenum Enzymes
Authors: Kirk Martin L. , Knottenbelt Sushilla , Habtegabre Abebe 
Published: September 2009

Abstract
Spectroscopic studies on two pyranopterin molybdenum enzymes, sulfite oxidase and xanthine oxidase, have been used to evaluate the results of detailed bonding calculations and provide insight into the reductive half reaction of these enzymes. Specifically, the nature of the reaction coordinate with respect to substrate oxidation appears to be under orbital control, with the inherent electronic structure of the active site playing a key role in the reactivity of these metalloenzymes.
Computational Methods: Heteropolyoxoanions
Authors: Poblet Josep M. , López Xavier 
Published: September 2009

Abstract

Possibly no other class of organic or inorganic compounds displays more versatility than polyoxometalates (POMs) (or polyoxoanions) with respect to electronic and molecular structures, properties, and applications. POMs attract the attention of scientists from many fields, such as catalysis, materials science, and medicine. More recently, POMs have also attracted the interest of computational chemists. This article describes some of the most relevant electronic properties for several of the most representative heteropolyoxoanions, such as the so‐called Keggin [XM
12
O
40
]

n
−

, Dawson [X
2
M
18
O
62
]

m
−

, and Preyssler [XP
5
W
30
O
110
]

q
−

anions. Density functional theory (DFT) methods have proven to be useful for the rationalization of many properties of POMs. In this article we illustrate some of them, often using the simple language of molecular orbitals.
Potential Energy Surfaces for Metal‐Assisted Chemical Reactions
Authors: Marino Tiziana , del Carmen Michelini Maria , Russo Nino , Sicilia Emilia , Toscano Marirosa 
Published: September 2009

AbstractThe potential energy surfaces for a series of metal‐assisted reactions have been investigated in the framework of density functional theory (DFT). The reported examples are representative of the difficulties encountered in the construction of reliable potential energy surfaces (PESs) when metal‐containing systems are involved. The results contribute to the elucidation of the elementary mechanisms underlying the activation processes of prototypical bonds in gas phase and in enzymatic environment.
Noble Gas Compounds: Reliable Computational Methods
Authors: Dixon David A. 
Published: September 2009

AbstractBecause of the general interest in the bonding in noble gas (Ng) compounds and the lack of experimental data coupled with large discrepancies, reliable theoretical calculations are very important for the prediction of their structures and thermodynamics. We describe an approach for the prediction of heats of formation to ±1 kcal mol−1(chemical accuracy) based on molecular orbital theory level using coupled cluster (CCSD(T), coupled cluster with single and double excitations plus a perturbative triples correction) theory extrapolated to the complete basis set (CBS) limit with the correlation‐consistent basis sets including relativistic effective core potentials (RECPs). Additional corrections to the valence correlation energies include core–valence (CV) correlation, molecular scalar relativistic corrections, atomic spin–orbit corrections, and zero‐point vibrational energies. Applications of this approach for the determination of the structure of XeF6, the heats of formation of the xenon fluorides and krypton fluorides, and the methyl cation affinities (MCAs) of the Ngs are described. XeF6is predicted to have C3vsymmetry only at the highest computational levels. The experimental heats of formation of XeF4and XeF6require significant revision. The predicted heats of formation for KrF4and KrF6show that it will be extremely difficult to synthesize these compounds. The calculations show that there are serious issues with the experimental MCAs of all of the Ngs except for Ne.
Gaussian Basis Sets for Quantum Mechanical (
QM
) Calculations
Authors: Peterson Kirk A. 
Published: September 2009

Abstract
In addition to the selection of a particular electronic structure method, the choice of basis set to use in an ab initio calculation can also strongly influence the accuracy of the results. The possibility of decoupling the errors associated with the chosen method and basis set is central to any systematic treatment of electronic structure. With this in mind, the availability, characteristics, and use of accurate Gaussian basis sets across the entire periodic table are reviewed with special emphasis to series of basis sets that improve in quality in a systematic fashion toward the complete basis set limit.
Diversity of Archaea
Authors: Swan Brandon K , Valentine David L 
Published: September 2009

AbstractThe Archaea are a group of microbes that form one of three domains of life on Earth. Studies with isolated strains have revealed an archaeal metabolic diversity rivaling that found within the domain Bacteria, and molecular surveys have revealed that archaea occupy a broader range of environments than was suspected based on the physiology of isolates. Archaea are also the most abundant and active microbial component in some environments, typically where their adaptations to chronic energy stress provide selective advantage over bacteria. Ongoing studies of uncultured archaea are likely to reveal important impacts on Earth's elemental and energy cycles.Key conceptsComparison of small subunit ribosomal RNA (16S rRNA) gene sequences and other cellular characteristics revealed that Archaea are a distinct group of microbes and one of three domains of life on Earth.The majority of archaeal diversity is composed of two kingdoms: the Crenarchaeota and Euryarchaeota.Most of the cultured archaea are ‘extremophiles’, or organisms that are adapted to living under extreme environmental conditions.The common ecological factor among the Archaea is their propensity to thrive under conditions of chronic energy stress.The ‘uncultured majority’ refers to the abundant, widespread, and highly diverse groups of archaea that currently lack cultured isolates.The metabolic functions of some uncultured archaea have been revealed by combining molecular, biochemical and geochemical techniques.
m
RNA
Stability
Authors: Bläsi Udo , von Gabain Alexander 
Published: September 2009

Abstract

The steady‐state level of a messenger
ribonucleic acid
(mRNA) is determined by both its rate of synthesis and degradation. The degradation of mRNA is an important tool employed by cells to control gene expression, and to adjust the level of protein synthesis in response to physiological needs. The degradation of mRNA in all organisms is mastered by a rather restricted number of endo‐ and exoribonucleases. Some of these enzymes are phylogenetically conserved across the three domains of life – bacteria, archaea and eukarya. This review provides a brief overview on the major factors and mechanisms involved in bacterial and eukaryal mRNA degradation.

Key concepts:

Enzymes and factors involved in mRNA decay in prokaryotes and eukaryotes.

Mechanisms of mRNA decay in pro‐ and eukaryotes.

Defective mRNAs and decay.

Noncoding RNAs and mRNA decay.
Vertebrate Neurogenesis: Cell Polarity
Authors: Zolessi Flavio R 
Published: September 2009

Abstract

During development, neurons are formed from epithelial cells that, after proliferation and cell fate decisions, must undergo a series of transitions in polarity to achieve the differentiated state. The fate of neural progenitors greatly depends on the interplay between cell cycle and neuroepithelial polarity. In this respect, two main processes appear to influence neurogenesis: (a) the asymmetrical inheritance of apical or basal compartments during the last cell division and (b) the interkinetic nuclear migration through gradients of signalling molecules. After a neuron is born, the differentiation process starts with a downregulation of epithelial polarity, followed by cell detachment and migration and the final acquisition of a neuronal morphology. All these transitions are based on extremely conserved molecular mechanisms, including polarity protein complexes and small GTPases. However, some important variations have been observed in different neuronal types and experimental conditions, which might represent a tip for the neuronal type differentiation iceberg.

Key concepts:

Origin of neurons in the central nervous system of the vertebrates.

Cellular organization of the primordium of the central nervous system.

Importance of cell divisions in the development of the central nervous system.

Relationship between cell polarity and the generation of neurons.

Symmetrical and asymmetrical cell divisions and their role in cell fate determination in the central nervous system.

Cell polarity and maintenance of neural progenitors.

Cell polarity and neuronal migration.

Cell polarity and neuronal differentiation.

Morphological transitions that lead to neuronal differentiation.

Distinction between cell polarity and orientation in neuronal differentiation.
Molecular Mimicry
Authors: Cunningham Madeleine White 
Published: September 2009

AbstractMolecular mimicry is structural, functional or immunological similarities shared between macromolecules found on infectious pathogens and in host tissues. Molecular mimicry plays an important role in immune responses to infection and in autoimmune diseases. Infection may induce autoimmune responses which attack and destroy body tissues or organs. Normally, the body is tolerant to self‐antigens which are present in individual tissues. In autoimmune disease, tolerance is abrogated to self‐antigens, and tissues or organs are destroyed by the immune system. Molecular mimicry of a self‐antigen by an infectious pathogen, such as bacteria and viruses, may trigger autoimmune disease due to a crossreactive immune response against the infection. Crossreactive antigen–antibody and T cell–antigen reactions are used to identify the mimicking macromolecules on the pathogen and in tissues or organs. These parameters define the concept of molecular mimicry.Key Concepts:There are three types of mimicry.Immunological mimicry between dissimilar epitopes on chemically different molecules has changed the concept that an antibody molecule must recognize only a single antigenic epitope.Although molecular mimicry was once thought by immunologists to be a ‘phenomenon’ or ‘nonspecific immune reaction’, mimicry is now considered to be a part of the normal immune system and plays an important role in protection against pathogens.Microbial infections may activate the immune system and lead to a loss of immune tolerance which could allow expansion of high avidity crossreactive B‐ or T‐cell clones which through molecular mimicry may lead to autoimmune disease.Mimicry has been shown to lead to the induction of autoantibodies which alter signalling in cells.
Immunoelectrophoresis
Authors: Levinson Stanley S 
Published: September 2009

AbstractImmunoelectrophoresis is a two‐stage process. Electrophoresis is conducted in the first stage and immunoprecipitation using antibodies against specific proteins in the second stage without removing the proteins from the separation media (usually agarose). Four types of immunoelectrophoresis (IEP) have been used: electroimmunoassay (EIA also called ‘rocket’ or ‘Laurell rocket’), classical IEP, immunofixation electrophoresis (IFE) and immunoprecipitation of proteins after capillary electrophoresis. The procedure used in most medical laboratories is IFE where the proteins are immunoprecipitated on the gel in a pattern that is similar to their location on routine agarose gel electrophoresis. This type of immunoelectrophoreisis is easier to interpret and more sensitive than the IEP that it replaced. The principles underlying each method and the strengths and weaknesses of each is described. Example of IEP and IFE for identifying monoclonal proteins in serum and urine and the relationship of the proteins to disease is discussed.Key conceptsImmunoelectrophoresis differs from blotting techniques because with IE the entire procedure is conducted in an agarose gel and blotting is not necessary.These techniques are based on the concept that near equivalency an antigen–antibody complex will precipitate and become trapped in the gel.Immunofixation electrophoresis (IFE) is preferred over immunoelectrophoresis because of its greater sensitivity and simpler interpretation characteristics.Immunofixation electrophoresis is largely used in medical or clinical laboratories for identifying abnormal monoclonal immunoglobulins associated with diseases of lymphocytes such as multiple myeloma.The abnormal protein bands identified on IFE line up with bands seen on routine agarose electrophoresis making interpretation simpler.Proteins in large concentration can cause prozoning on IFE causing more difficulty in interpretation.IFE is widely used in medical laboratories for identifying monoclonal free light chains in urine, called Bence Jones proteins.IFE can also be used for identifying oligoclonal banding in cerebrospinal fluid.
Thrombin
Authors: Thiagarajan P , Narayanan A S 
Published: September 2009

Abstract

Thrombin
is a
serine protease
that converts fibrinogen to fibrin in blood coagulation. The precursor of
thrombin
,
prothrombin
(inactive zymogen), is one of the several coagulation proteins containing γ‐carboxyglutamic acid.
Prothrombin
is synthesized in the liver and secreted into blood circulation, and it is activated by vascular injury by limited proteolysis following upstream activation of the coagulation cascade.
Thrombin
activity is regulated by serum inhibitors and by its own action. With its procoagulant and anticoagulant functions it plays a central role in thrombosis and haemostasis, and it is an agonist for a number of cellular responses during inflammation and wound repair. Many diseases including stroke and myocardial infarction involve thrombosis; therefore, thrombin is a preferred target of antithrombotic drugs. Drugs available to block thrombin action include heparins, hirudins (lepirudin and bivaliruidin), vitamin K antagonists and a new generation of direct
thrombin
inhibitors such as dabigatran and argatroban.

Key concepts

Thrombin is a serine protease that converts fibrinogen to fibrin and plays a crucial role in hemostasis and thrombosis.
Bacterial Membrane Transport: Organization of Membrane Activities
Authors: Padan Etana 
Published: September 2009

Abstract

Bacteria have transport systems enabling them to accumulate needed nutrients, extrude unwanted by‐products and modify their cytoplasmic content of protons and salts so as to maintain a composition conducive to growth and development. Most bacterial transport systems resemble their counterparts in eukaryotic cells, and similar principles operate in both cell types. Because bacterial transporters are often easier to deal with experimentally, they have become important models for their eukaryotic brethren. The recent determination of the crystal structure of several bacterial transporters including ones that share homology with human transporters that are important in health and disease has been a major breakthrough. It opened the way both to the understanding of the mechanism of active transport as well as to rational drug design.

Key concepts

Cytoplasmic membrane separates the cytoplasm from the cell‐environment and at the same time communicates between these compartments by transducing signals and transporting molecules and ions across the membrane.

Channels facilitate the passive transport of molecules or ions across the membrane.

Transporters couple energy to actively transport molecules or ions across the membrane.

Primary transport system couples transport to chemical or light energy.

Secondary transport system couples transport to chemiosmotic energy.

Chemiosmotic circuit couples several secondary‐ and primary transporters in a biological membrane.

A virtual proton pump emerges from combining transport and metabolism.

The proton motive force or the electrochemical gradient of protons across the membrane provides a reservoir of potential energy to be used in all forms of energy‐transduction across the membrane.

Crystal structure of membrane proteins are critical for understanding the mechanism of transporters and for drug design for transporters involved in human's health and disease.