bluuebunny/crossref_metadata_2025 huggingface dataset:
Fictions télévisuelles et idéologies en Indonésie
Authors: Zaini-Lajoubert Monique
Published: September 2009

Monique Zaini-Lajoubert

Indonesian television has broadcast fiction films since its inception in 1962. These broadcasts have become known since 1985 under the name sinetron (sinema elektronik). The term's meaning seems to have changed with time. Today it can mean any kind of television film, fiction or non-fiction, produced in Indonesia or abroad. This article studies Indonesian fiction films for television which, since the creation of so-called " private " television since the end of the 1980s, have experienced tremendous development. It tries to highlight a particular aspect of the sinetron, as vehicles of ideologies, not only under the New Order, but also since Reformasi. It deals particularly with sinetron such as Losmen, Terjebak, Reuni, Penari or Bingkisan untuk Presiden.
Un lac autour du Borobudur?
Authors: Dumarçay Jacques
Published: September 2009

Jacques Dumarçay

An article published in the Journal of Volcanology and Geothermal Research in 2000 brought new arguments in support of the theory that the Borobudur temple once was surrounded by a lake - a theory which has long been favoured by archaeologists, notably Nieuwenkamp in 1931. J. Dumarçay brings to the fore archaeological evidence, discovered during the 1950s to 1970s (buildings, tombs, ceramics, stupas, and plants) which show that the presence of a lake seems impossible. However, it had probably been planned, during the first phase of the construction of the Borobudur, to divert the course of a nearby river (the Kali Silang) in order to establish a moat around the monument, traces of which are still found on its northern side.
L'énigmatique inscription musulmane du maqâm de Kediri (Xe s. H./XVI s. E.C)
Authors: Guillot Claude , Kalus Ludvik
Published: September 2009

Claude Guillot

In the Kampung Sentana Gedong of Kediri, East- Java, an old Arabie inscription can be seen on a wall of a XVIth century ruined building. The text refers to a certain Near-Eastern imam and shaykh whose name was voluntarily erased and who probably died during the decade 920 H (1514-1523 A.D.). Convinced that such a prominent "islamizator" could not have been ignored by local chronicles, the authors propose an hypothesis to solve the enigma of this early testimony of islamic presence in that region. The building would have been erected by Sunan Kudus in order to commemorate his victory over the "pagan" kingdom of Majapahit which took place around 1527, and precisely in Kediri. They assume that the imam refered to in the inscription might be Sunan Kudus' father, known as Rahmatullahi, who held the function of imam at Demak, died on the battlefield in the second attack he launched against Majapahit in the early 1520's and was buried by the Mosque at Demak. By the way of this inscription, Sunan Kudus would have associated his father's memory to his own success over "Paganism".
A Tentative Interpretation of the Chinese Inscription (1231) Engraved on a Bronze Gong Recovered in Muara Jambi {Central Sumatra)
Authors: Lombard-Salmon Claudine
Published: September 2009

Claudine Salmon

L'histoire du gong et de sa diffusion en Asie en général et en Insulinde en particulier reste encore très mal connue. Dans un travail récent, Inge Skog concluait qu'il y a très peu d'information sur cet instrument de musique à Java avant le XIVe siècle. Or, la mise au jour d'un «gong militaire» pourvu d'une inscription chinoise datée des Song du Sud (1231) à l'intérieur du complexe d'un temple apparemment bouddhique de Muara Jambi fait remonter l'introduction de l'instrument plus loin dans le temps. Cette découverte assez extraordinaire - à notre connaissance, aucun autre gong daté n'a été retrouvé en Chine même pour les hautes époques - a permis de reconsidérer l'histoire de cet instrument dans un contexte géographique allant de la Chine à l'Insulinde. L'article envisage successivement le cadre et les circonstances de la découverte qui remonte au début des années 1980, le gong lui-même d'un point de vue technique, en le comparant aux plus anciens gongs retrouvés en Chine mais aussi dans des épaves de bateaux d'Insulinde, sa technique de fabrication, et l'usage de l'instrument dans la Chine des Song; enfin l'inscription elle même, son interprétation et les hypothèses concernant le lieu où le préfet, qui est à l'origine de l'inscription et du don, a pu être en poste - en Chine ou à Srivijaya - et, par voie de conséquence, sur les liens entre ces deux pays.
A Japanese Soldier's Ethnography of Molu Island (Tanimbar) : Ken Sasaki's Account (1944-1945)
Authors: Suzuki Peter T , Watanabe Reiger Reiko
Published: September 2009

Peter T. Suzuki

Ken Sasaki est un soldat japonais qui, de juin 1944 à mai 1945, pendant la Guerre du Pacifique, fut posté sur l'île de Molu, dans le petit archipel des Tanimbar, aux Moluques. Il connut l'épreuve du feu et, avec ses six camarades, demeura constamment en alerte. Il avait beaucoup de temps libre, cependant, qu'il mit à profit pour receuillir des informations sur la population de Molu, ses origines, sa langue, ses coutumes et son artrisanat. Ses notes, abondamment illustrées de ses propres dessins, constituent une importante contribution à l'ethnographie de la région.
Gouw Peng Liang's Novella, Lo Fen Koei : Patrons and Women. An Account of the Peranakan Chinese Community of Java in the Late 19th Century
Authors: Worsley Peter
Published: September 2009

Peter Worsley

Lo Fen Koei, roman pulié en 1803 dans un quotidien de Batavia par le célèbre journaliste Gouw Peng Liang, connut une popularité suffisante pour être publié sous forme de livre la même année, pour circuler aussi sous forme de manuscrit dans une version différente et pour être encore adapté à la scène. L'histoire, celle des turpitudes d'une fermier d'opium de Java Centre, était tirée de faits divers publiés dans le même journal, le Bintang Betawi, mais la dramatisation des faits et des personnages, la mise en contraste des comportements et la morale des événements transformés en conte, appartiennent à l'auteur. Plus que des aperçus de la vie des Chinois à Java en ce tournant de siècle, on peut y lire assez précisément la façon dont la communauté chinoise se représentait le monde dans lequel elle vivait et comment elle jugeait ce qu'il aurait dû être.
The sign of Protesilaos
Authors: Nagy Gregory
Published: September 2009

The sign of Protesilaos (pp. 207-213)

La valeur sémantique du mot σήμα, dans le double sens de «signe» et de «tombe d'un héros», aide à expliquer la stratégie narrative d'Hérodote, qui termine son Ίστορίη avec l'histoire d'un prodige, présenté comme envoyé du monde des héros épiques au monde des hommes contemporains. La clef d'interprétation de cette histoire est le mot τάριχος, qui se réfère à la conservation de la nourriture dans le domaine de la vie quotidienne, ainsi qu'à l'immortalisation du corps dans le domaine du rituel sacré.
Entre la honte et la gloire
Authors: Vernant Jean-Pierre
Published: September 2009

Entre la honte et la gloire (pp . 269-299)

Paradoxe de l'éducation Spartiate: de l'enfance à l'adolescence, le dressage des jeunes garçons, en son extrême rigueur, vise à les soumettre entièrement aux normes civiques. Mais cet apprentissage des règles qui leur ouvrent la voie des honneurs s'opère, sous le patronage d'Artémis Orthia, à travers un cursus d'épreuves où chacun, pour démontrer sa capacité à devenir un citoyen accompli, doit manifester son excellence dans des pratiques que les adultes tiennent pour déviantes, indignes, scandaleuses. La conformité au modèle de l'homme d'honneur passe par l'entrainement dans des conduites, des façons de vivre, de manger, de se vêtir aberrantes, honteuses, deshonorantes qui rapprochent les jeunes des hilotes. Comme si pour accéder à l'identité sociale, il fallait d'abord se mettre à distance, se montrer et se reconnaître différents de ce qu'on a l'obligation de devenir, se familiariser avec les violences, les fraudes, les vilenies, les bassesses auxquelles il faudra renoncer du jour où l'on entrera dans le cercle des adultes. Le prix à payer, pour atteindre l'idéal civique et guerrier, pour devenir un «semblable», un «égal», c'est d'endosser et d'explorer, pendant la période probatoire, des formes d'altérité, dans leurs aspects parfois extrêmes.
Le satyre casseur
Authors: Berard Claude
Published: September 2009

Le satyre casseur (pp. 75-92)

Critiquant sa première lecture d'inspiration religieuse, l'auteur propose une nouvelle solution dans un cadre historique et politique. La fureur iconoclaste du satyre s'inscrit ainsi dans une dénonciation des valeurs éthiques traditionnelles de la cité grecque. Le Peintre de Géras rédige en fait un pamphlet contre la Καλοκαγαθία et choisit de porter le lieu de la contestation dans l'Agora d'Athènes. Tout le programme du vase est organisé selon un système antithétique qui oppose ordre et sagesse à la fantaisie sans bornes et au tohu-bohu démonique: ainsi l'inscription καλός sur la vasque du loutérion ne fait que souligner la laideur grotesque de l'oiseau-phallus.
Dulce et decorum pro patria mori
Authors: Hoffmann Herbert
Published: September 2009

Dulce et decorum pro patria mori (pp. 127-135)

A propos de l'image décorant le col d'un rhyton à tête de bélier du Musée de Boston, on se propose de dépasser le niveau, purement iconographique, de l'identification des personnages pour en retrouver le sens global en envisageant le vase dans une perspective anthropologique. L'idéologie péricléenne de la mort glorieuse de l'hoplite pour la cité et du sacrifice paradigmatique consenti par les mères donne la clef de cette image représentant un jeune homme assis devant une femme qui lui tend ses armes.
La condition juridique des citoyens Athéniens frappés par le décret du 322: άτιμοι ou φυγάδες ? "
Authors: Poddighe Elisabetta
Published: September 2009

La condition juridique des citoyens Athéniens (pp . 27 1-283)

La mesure prise par Antipatros avait privé un nombre non négligeable d'Athéniens de la politeia; une bonne partie de ces Athéniens, en outre, avaient été poussés à l'exil, peut-être même de force. La situation s'étant modifiée, ces exilés rentrèrent dans la polis; dans les sources il apparaît que l'appelation de φυγάδες leur restait; Cette qualification privilégiait le sens de la dureté d'une existence vécue matériellement par rapport à celui d'une condition juridique qui caractérisait de la même façon les hommes qui -s'étant trouvés dans le même statut- étaient néanmoin restés sur le territoire de la polis.
Women and the formation of the athenian City-State [The evidence of burial customs]
Authors: Houby-Nielsen Sanne
Published: September 2009

Women and the Formation ofthe Athenian City-State (pp. 233-260)

Une part essentielle de nos connaissances sur les premiers temps de la cité athénienne provient de l'étude des rites funéraires. Or, cette source d'information pourrait avoir été largement influencée par les pratiques et conceptions des femmes, dans la mesure où ce sont les femmes qui, vraisemblablement, choisissaient et disposaient les offrandes que l'on trouve dans les tombes. De plus, les grands traits de la répartition des différents types de nécropole autour de l'espace urbain émergent dès l'époque géométrique tardive et expriment une idéologie civique du «genre» où femmes, enfants et hommes contribuaient tous à manifester la nature exemplaire de la société et de la cité athéniennes. Cet article souligne ainsi la difficulté de toute tentative de séparation stricte entre «état» et «société» dans la cité antique et, de ce fait, d'exclusion des femmes, ainsi que des enfants et autres groupes dépourvus d'accès à la parole politique, du processus de formation de l'état.
L'expression du temps sur les stèles funéraires attiques
Authors: Hoffmann Geneviève
Published: September 2009

L'expression du temps sur les stèles funéraires attiques (pp. 19-43)

Les stèles attiques de l'époque archaïque et classique ont pour finalité de perpétuer la mémoire du défunt en l'incluant dans une catégorie digne d'admiration. Pour ce faire, l'espace-temps de la représentation prend sens dans le choix des accessoires, par le mouvement, les gestes ainsi que par l'échange établi entre les personnages ou avec le passant. A l'époque archaïque, l'accent est mis sur l'acte à accomplir dans un temps d'effraction ; les monuments classiques soulignent la solidarité des générations. Dans un cas, le spectateur est témoin de l'excellence du disparu ; dans l'autre, il est inclus dans le cercle du deuil et de la compassion.
Temps de l'énonciation, temps de l'action [Représentations chinoises]
Authors: Alleton Viviane
Published: September 2009

Temps del'énonciation, temps de l'action (pp. 81-95)

Les représentations du temps dans l'espace chinois à travers l'histoire furent multiples et complexes. On a cependant tenté de repérer quelques traits remarquables. Les événements, de la sphère privée aussi bien que publique, sont datés de façon précise. L'année est rythmée selon un calendrier solaire pour les activités agricoles, tandis que la vie sociale s'organise d'après un calendrier lunaire. Au-delà, la coupure historique créée par l'avènement de tout nouveau souverain segmente le temps long. Dans les activités humaines, la réflexion sur l'action est centrée sur la notion de «moment opportun». Dans l'univers des textes, où le passé est révéré en tant qu'il est canonisé dans des œuvres majeures, on observe un contraste entre le temps ouvert des citations et l'irréversibilité du poème ou de la calligraphie. Enfin, il importe d'insister sur le fait qu'en dépit de l'absence de toute conjugaison la langue chinoise dispose d'un ensemble de procédés pour exprimer le temps dans toutes ses dimensions.
L'historien mésopotamien et l'événement
Authors: Glassner Jean-Jacques
Published: September 2009

L 'historien mésopotamien et l'événement (pp. 97-1 17)

La question posée est celle de la construction de l'événement par l'historien mésopotamien. On voit qu'un fait prend le statut d'événement historique lorsqu'il s'inscrit dans une série homogène de faits similaires au sein de laquelle il dévoile une variation conjoncturelle. Mais il manque à l'historien mésopotamien une qualité essentielle, la critique des sources.
Beobachtungen zu den Exekias-Signaturen
Authors: Mommsen Heide
Published: September 2009

Beobachtungen zu den Exekias-Signaturen (pp. 39-55)

Des signatures attestant le nom d'Exékias sont aujourd'hui connues sur 15 vases. Trois, voire vraisemblablement quatre amphores comportent une signature double et trois vases peints par Exékias attestent par la signature qu'il en est également le potier. La forme de chacun de ces vases représente une innovation et le système décoratif est intégré dans la composition ordonnée. Deux amphores portant l'inscription EXSEKIAS EPOIESE, œuvres d'un peintre du groupe E, prouvent par leur forme caractéristique qu'Exekias exerçait déjà le métier de potier vers le milieu du Vie siècle. Un groupe de cinq coupes de Siana, datées entre 560 et 550, n'ont pas été décorées par Exékias. Les signatures ne sont d'ailleurs pas de sa main. Enfin, la forme conventionnelle de ces coupes ne permet pas de dire si elles sont l'œuvre du potier Exékias.
L'inscription comme élément décomposition
Authors: Strawczynski Nina
Published: September 2009

L 'inscription comme élément de composition (pp. 107-121)

L'analyse de trois vases d'époques différentes permet de montrer comment certains peintres utilisent les inscriptions en interaction avec la composition pour enrichir la signification de la scène. Clitias sur le Vase François met ainsi en évidence certains objets et incite le spectateur à un travail de mise en relation entre les scènes de son vase ou avec la tradition iconographique. C'est le cas en particulier des deux scènes principales de l'avers du vase, où les inscriptions soulignent le contraste entre le mariage de Pelée et la poursuite de Troïlos. Lydos, sur un plat conservé à Athènes, utilise les inscriptions pour compléter l'interprétation induite par la scénographie et dévoile ainsi l'interaction entre les sphères mythiques et quotidiennes. Un siècle plus tard, le peintre d'Érétrie, par l'ajout d'inscriptions dans des scènes de départ de guerrier apparemment banales, met en relation les destinées d'Achille et de Patrocle, représentées sur chaque face d'un canthare. Dans ces trois exemples, les inscriptions sont utilisées conjointement à la composition et jouent avec elle pour enrichir la signification de l'épisode mythique représenté. Ce travail graphique des peintres prouve combien ils sont loin du simple récit ou de l'illustration d'une légende.
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.
Textes et fragments grecs de Palmyre
Authors: Al-As'ad Khaled , Yon Jean-Baptiste
Published: September 2009

The publication of these modest Greek and bilingual texts allows to surmise that certain phrases and expressions were more common in Palmyra than it is usually thought. Inscriptions concerning foundation or concession of tombs are also included, as well as new evidence of the close links between Palmyrenes and the Severian Emperors.
Abinitioand Semiempirical Methods
Authors: Gorelsky Serge I.
Published: September 2009

Ab 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

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

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

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

The 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

Because 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

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

The 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 concepts

Comparison 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

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

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

Molecular 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

Immunoelectrophoresis 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 concepts

Immunoelectrophoresis 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

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

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.
DNA
Sequence Analysis
Authors: Gojobori Takashi , Nakagawa So , Clemente Jose C
Published: September 2009

Recent advances in
deoxyribonucleic acid
(DNA) sequencing technology have produced a massive amount of nucleotide sequences, which are stored in DNA databanks and genomic data repositories. Furthermore, comprehensive analyses of transcriptional and genomic elements have uncovered an elaborate system of gene expression that broadens our understanding of fundamental biological phenomena. The analysis of DNA data has therefore become essential to predict gene function or detect regulatory motifs through comparative studies. In this article, DNA databases, homology search tools and sequence alignment methods are surveyed. The concept of distance between genes and how to calculate this measure using DNA or amino acid sequences and introducing several commonly used techniques for phylogenetic analysis and tree evaluation are also described.

Key concepts

Advances in DNA sequencing technology have produced an unprecedented amount of sequence data.

The DNA Data Bank of Japan (DDBJ), the European Bioinformatics Institute (EBI) and the National Center for Biotechnology Information (NCBI) are the three major sequence data repositories. They exchange data periodically, and maintain various services for data search and retrieval.

Similarity searching, alignment of sequences, prediction of function and reconstruction of the evolutionary history (phylogenetic tree) of a group of species are among the most commonly used techniques for sequence analysis.

BLAST (similarity searching), ClustalW (sequence alignment), Pfam (protein domains) and TRANSFAC (transcription factors) are popular tools and resources.

The genetic distance, a measure of evolutionary similarity, is usually calculated as the number of nucleotide or amino acid differences (substitutions) among sequences. Nucleotide substitutions are synonymous (not affecting the codified amino acid) or nonsynonymous (triggering an amino acid change).

Distance‐ and character‐based methods can be used to reconstruct phylogenetic trees. Distance‐based methods reconstruct the tree from an estimation of the evolutionary distance among taxa. Character‐based methods derive the phylogeny directly from the observable state of characters in the taxa.

The bootstrap method is commonly used to determine the quality of an inferred phylogeny.
Comparative Genomic Hybridization
Authors: Tachdjian Gérard
Published: September 2009

Comparative genomic hybridization (CGH) is a modified
in situ
hybridization technique which allows detection and mapping of DNA (
deoxyribonucleic acid
) sequence copy differences between two genomes. In CGH analysis, two differentially labelled genomic DNA (study and reference) are cohybridized to normal metaphase spreads or to microarray. Chromosomal locations of copy number changes in the DNA segments of the study genome are revealed by a variable fluorescence intensity ratio along each target chromosome or DNA sequences. Thus, CGH allows detection and mapping of DNA sequence copy differences between two genomes in a single experiment. Since its development, CGH has been applied as a research tool in the field of cancer cytogenetics to identify genetic changes in many previously unknown regions. CGH is also a powerful tool for detection and identification of unbalanced chromosomal abnormalities in prenatal, postnatal and preimplantation diagnostics. Array CGH is a high‐resolution technique to detect chromosomal DNA copy number variations at a genome‐wide scale.

Key concepts

Comparative genomic hybridization is a modified
in situ
hybridization technique.

CGH allows detection and mapping of DNA sequence copy differences between two genomes.

In CGH analysis, two differentially labelled genomic DNA segments (study and reference) are cohybridized to normal metaphase spreads or to mapped DNA sequences or oligonucleotides arrayed onto glass slides (array CGH).

Chromosomal locations of copy number changes in the DNA segments of the study genome are revealed by a variable fluorescence intensity ratio along each target chromosome.

In CGH on chromosomes, genetic changes are detected and mapped on chromosomes.

CGH allows the detection and characterization of whole and partial aneuploidies.

CGH has been widely used for the study of chromosomal imbalances in tumours.

An important contribution of CGH to cancer research has been in pinpointing putative locations of cancer genes.

In clinical genetics, CGH is increasingly used in diagnosing unbalanced chromosomal rearrangements.

Since its development, CGH has been applied mostly as a research tool in the field of cancer cytogenetics, but it is also used in clinical genetics.
History of Antiulcer Drugs
Authors: Fuccio Lorenzo , Leonardo Henry Eusebi , Bazzoli Franco
Published: September 2009

The therapy of peptic ulcer disease has progressively changed in the last two centuries. Major discoveries were achieved by the possibility to directly visualize the first part of the gastrointestinal tract with endoscopy and by the availability of potent antisecretory agents. Then, since

Helicobacter pylori

was discovered, the cause of this disease was understood and the optimal therapy was found. The cure of the infection was not only able to heal the ulcer but also to cure the disease, interrupting its relapsing behaviour. Initially, dual therapy, a combination of a proton pump inhibitor with an antibiotic, demonstrated an overall efficacy for the eradication of
H. pylori
better than monotherapy, but still not satisfactory. Finally, a triple therapy of proton pump inhibitor, clarithromycin, and either amoxicillin or metronidazole, has been the most widely recommended eradication treatment.

Key concepts

Neutralization of gastric acidity heals peptic ulcer but does not prevent relapse of
Helicobacter pylori
‐related ulcer.

H. pylori

has been clearly related to gastritis, peptic ulcer (gastric and duodenal ulcer), gastric lymphoma and cancer.

Eradication of

H. pylori

infection heals and prevents the peptic ulcer relapse.

The triple therapy of proton pump inhibitor and two antibiotics (clarithromycin and either amoxicillin or metronidazole) is the most widely recommended eradication treatment for

H. pylori

infection.
Bioethics: Institutionalization of
Authors: Engelhardt HT , Iltis Ana Smith , Jotterand Fabrice
Published: September 2009

Bioethics is a recognized discipline in the academy, an established practice within the clinic and a source of guidance for healthcare policy and the conduct of human research. As a complex of theoretical and practical undertakings, bioethics now commands an officially recognized cluster of norm‐setting and behaviour‐guiding roles that have become institutionalized elements of the scholarly, clinical, human research and public policy establishment. The integration of the antecedents of bioethics into these settings began in the 1960s but these activities were recognized under this name only at the end of the 1970s. By 1979, there was an established literature, numerous individuals who called themselves bioethicists, academic programs engaged in bioethics. Attention to bioethics internationally continues to grow, particularly as biotechnological developments raise new questions and concerns.

Key Concepts

The antecedents of bioethics emerged in the 1960s, and then the field took shape under this rubric in the 1970s.

Awareness of past abuses of human research subjects and the need to conduct more research to secure progress in medicine led to a focus on research ethics and the regulation and oversight of research.

Cultural shifts in the 1960s and 1970s that emphasized individual rights led to discussions about patients’ rights and patient‐driven decisions.

The secularization of U.S. society in the 1960s created space for discussions of medical morality among secular scholars who sought a secular source for moral guidance.

Bioethicists provide clinical and research ethics consultations, teach and conduct research in the academy and are involved in the creation of public policy.

Bioethics continues to seek substantive moral insight from secular sources.