Chemoinformatics Research at the University of Sheffield: A History and Citation Analysis

This paper reviews the work of the Chemoinformatics Research Group in the Department of Information Studies at the University of Sheffield, focusing particularly on the work carried out in the period 1985-2002. Four major research areas are discussed, these involving the development of methods for: substructure searching in databases of three-dimensional structures, including both rigid and flexible molecules; the representation and searching of the Markush structures that occur in chemical patents; similarity searching in databases of both two-dimensional and three-dimensional structures; and compound selection and the design of combinatorial libraries. An analysis of citations to 321 publications from the Group shows that it attracted a total of 3725 residual citations during the period 1980-2002. These citations appeared in 411 different journals, and involved 910 different citing organizations from 54 different countries, thus demonstrating the widespread impact of the Group's work

First principles calculation of vibrational Raman spectra in large systems: signature of small rings in crystalline SiO2

We present an approach for the efficient calculation of vibrational Raman intensities in periodic systems within density functional theory. The Raman intensities are computed from the second order derivative of the electronic density matrix with respect to a uniform electric field. In contrast to previous approaches, the computational effort required by our method for the evaluation of the intensities is negligible compared to that required for the calculation of vibrational frequencies. As a first application, we study the signature of 3- and 4-membered rings in the the Raman spectra of several polymorphs of SiO2, including a zeolite having 102 atoms per unit cell.Comment: 4 pages, 2 figures, revtex4 Minor corrections; accepted in Phys. Rev. Let

Inventory and new records of Polychaete species from the Cap Bon peninsula , North East coast of Tunisia, Western Mediterranean Sea

An inventory of polychaete species is presented from the north-east coast of Tunisia with an historic review of the previous literature from Tunisian coasts. Altogether 40 families, 146 genera, and 238 species are currently known from the area, of which 86 taxa, 4 families (Chrysopetalidae, Pilargidae, Protodrilidae and Saccocirridae) and 40 genera (Saccocirrus, Protodrilus, Parathelepus, Thelepus, Petta, Isolda, Brada, Tharyx, Paraprionospio, Jasmineira, Hypsicomus, Euchone, Pseudobranchiomma, Laonome, Galathowenia, Lugia, Pseudomystides, Protomystides, Pirakia, Mysta, Eurysyllis, Parapionosyllis, Streptosyllis, Paraehlersia, Sigambra, Ancistrosyllis, Kefersteinia, Chrysopetalum, Bhawania, Fimbriosthenelais, Subadyte, Panthalis, Dorvillea, Scalibregma, Paradoneis, Cirrophorus, Metasychis, Websterinereis, Euniphysa and Mastobranchus) are new additions to the polychaete fauna of Tunisia. The list, which provides a synthesis of the regional taxonomic work, including coastal areas from Sidi Daoud to the area of Menzel Hurr (Cap Bon Peninsula, Western Mediterranean Sea), can serve as a baseline for future studies

Melting and Pressure-Induced Amorphization of Quartz

It has recently been shown that amorphization and melting of ice were intimately linked. In this letter, we infer from molecular dynamics simulations on the SiO2 system that the extension of the quartz melting line in the metastable pressure-temperature domain is the pressure-induced amorphization line. It seems therefore likely that melting is the physical phenomenon responsible for pressure induced amorphization. Moreover, we show that the structure of a "pressure glass" is similar to that of a very rapidly (1e+13 to 1e+14 kelvins per second) quenched thermal glass.Comment: 9 pages, 4 figures, LaTeX2

Quicksort with unreliable comparisons: a probabilistic analysis

We provide a probabilistic analysis of the output of Quicksort when comparisons can err.Comment: 29 pages, 3 figure

Semipurity of tempered Deligne cohomology

In this paper we define the formal and tempered Deligne cohomology groups, that are obtained by applying the Deligne complex functor to the complexes of formal differential forms and tempered currents respectively. We then prove the existence of a duality between them, a vanishing theorem for the former and a semipurity property for the latter. The motivation of these results comes from the study of covariant arithmetic Chow groups. The semi-purity property of tempered Deligne cohomology implies, in particular, that several definitions of covariant arithmetic Chow groups agree for projective arithmetic varieties

Search for surface magnetic fields in Mira stars. First detection in chi Cyg

In order to complete the knowledge of the magnetic field and of its influence during the transition from Asymptotic Giant Branch to Planetary Nebulae stages, we have undertaken a search for magnetic fields at the surface of Mira stars. We used spectropolarimetric observations, collected with the Narval instrument at TBL, in order to detect - with Least Squares Deconvolution method - a Zeeman signature in the visible part of the spectrum. We present the first spectropolarimetric observations of the S-type Mira star chi Cyg, performed around its maximum light. We have detected a polarimetric signal in the Stokes V spectra and we have established its Zeeman origin. We claim that it is likely to be related to a weak magnetic field present at the photospheric level and in the lower part of the stellar atmosphere. We have estimated the strength of its longitudinal component to about 2-3 Gauss. This result favors a 1/r law for the variation of the magnetic field strength across the circumstellar envelope of chi Cyg. This is the first detection of a weak magnetic field at the stellar surface of a Mira star and we discuss its origin in the framework of shock waves periodically propagating throughout the atmosphere of these radially pulsating stars. At the date of our observations of chi Cyg, the shock wave reaches its maximum intensity, and it is likely that the shock amplifies a weak stellar magnetic field during its passage through the atmosphere. Without such an amplification by the shock, the magnetic field strength would have been too low to be detected. For the first time, we also report strong Stokes Q and U signatures (linear polarization) centered onto the zero velocity (i.e., at the shock front position). They seem to indicate that the radial direction would be favored by the shock during its propagation throughout the atmosphere.Comment: 9 pages, 4 figures accepted by Astronomy and Astrophysics (21 November 2013

Irradiation du petit bassin et fonction ano-rectale.

peer reviewedLe traitement adjuvant des cancers du rectum a pour buts de stériliser la maladie résiduelle infra-clinique et d’améliorer le contrôle local. Depuis plus de 20 ans, des milliers de malades ont été inclus dans des études randomisées, visant d’abord à mettre en évidence un gain de survie et une réduction des récidives loco-régionales, en relation avec la radiothérapie pré- ou postopératoire, combinée ou non à la chimiothérapie. Les conséquences en termes de qualité de vie de ces traitements ont pourtant été peu étudiées, et la tolérance fonctionnelle du néo-rectum et de l’appareil sphinctérien à la radiothérapie restent mal connues [1]. Les difficultés liées à l’étude des effets de l’irradiation sur les tissus normaux, ainsi que la variabilité inter-individuelle de la réponse à la radiothérapie, s’ajoutent et rendent le sujet plus complexe encore. Les radiothérapeutes adaptent leur technique afin de réduire autant que possible la dose administrée aux tissus normaux avoisinant la tumeur. Dans le cas de l’irradiation du petit bassin, c’est l’intestin grêle qui a longtemps été considéré comme la structure à risque de complications, alors que l’atteinte du sphincter anal était rarement mentionnée [2]. Malgré les répercussions importantes de la dysfonction ano-rectale sur la qualité de vie des malades, l’atteinte du sphincter anal par la radiothérapie est restée un aspect négligé du traitement adjuvant des cancers du petit bassin [3]. Cet article a pour but, à travers une revue de la littérature, de mettre en évidence les effets qualitatifs et quantitatifs de la radiothérapie sur la fonction du sphincter anal, ainsi que de proposer une modification de la technique actuelle d’irradiation des cancers du bas rectum

Vaccination with murid herpesvirus-4 glycoprotein B reduces viral lytic replication but does not induce detectable virion neutralization

Herpesviruses characteristically disseminate from immune hosts. Therefore in the context of natural infection, antibody neutralizes them poorly. Murid herpesvirus-4 (MuHV-4) provides a tractable model with which to understand gammaherpesvirus neutralization. MuHV-4 virions blocked for cell binding by immune sera remain infectious for IgG-Fc receptor+ myeloid cells, so broadly neutralizing antibodies must target the virion fusion complex – glycoprotein B (gB) or gH/gL. While gB-specific neutralizing antibodies are rare, its domains I+II (gB-N) contain at least one potent neutralization epitope. Here, we tested whether immunization with recombinant gB presenting this epitope could induce neutralizing antibodies in naive mice and protect them against MuHV-4 challenge. Immunizing with the full-length gB extracellular domain induced a strong gB-specific antibody response and reduced MuHV-4 lytic replication but did not induce detectable neutralization. gB-N alone, which more selectively displayed pre-fusion epitopes including neutralization epitopes, also failed to induce neutralizing responses, and while viral lytic replication was again reduced this depended completely on IgG Fc receptors. gB and gB-N also boosted neutralizing responses in only a minority of carrier mice. Therefore, it appears that neutralizing epitopes on gB are intrinsically difficult for the immune response to target