ISPIDER Central: an integrated database web-server for proteomics

Despite the growing volumes of proteomic data, integration of the underlying results remains problematic owing to differences in formats, data captured, protein accessions and services available from the individual repositories. To address this, we present the ISPIDER Central Proteomic Database search (http://www.ispider.manchester.ac.uk/cgi-bin/ProteomicSearch.pl), an integration service offering novel search capabilities over leading, mature, proteomic repositories including PRoteomics IDEntifications database (PRIDE), PepSeeker, PeptideAtlas and the Global Proteome Machine. It enables users to search for proteins and peptides that have been characterised in mass spectrometry-based proteomics experiments from different groups, stored in different databases, and view the collated results with specialist viewers/clients. In order to overcome limitations imposed by the great variability in protein accessions used by individual laboratories, the European Bioinformatics Institute's Protein Identifier Cross-Reference (PICR) service is used to resolve accessions from different sequence repositories. Custom-built clients allow users to view peptide/protein identifications in different contexts from multiple experiments and repositories, as well as integration with the Dasty2 client supporting any annotations available from Distributed Annotation System servers. Further information on the protein hits may also be added via external web services able to take a protein as input. This web server offers the first truly integrated access to proteomics repositories and provides a unique service to biologists interested in mass spectrometry-based proteomics

Superfluid Spin-down, with Random Unpinning of the Vortices

The so-called ``creeping'' motion of the pinned vortices in a rotating superfluid involves ``random unpinning'' and ``vortex motion'' as two physically separate processes. We argue that such a creeping motion of the vortices need not be (biased) in the direction of an existing radial Magnus force, nor should a constant microscopic radial velocity be assigned to the vortex motion, in contradiction with the basic assumptions of the ``vortex creep'' model. We point out internal inconsistencies in the predictions of this model which arise due to this unjustified foundation that ignores the role of the actual torque on the superfluid. The proper spin-down rate of a pinned superfluid is then calculated and turns out to be much less than that suggested in the vortex creep model, hence being of even less observational significance for its possible application in explaining the post-glitch relaxations of the radio pulsars.Comment: To be published in J. Low Temp. Phys., Vol. 139, May 2005 [Eqs 11, 15-17 here, have been revised and, may be substituted for the corresponding ones in that paper

Comparison of the biotypes of Yersinia enterocolitica isolated from pigs, cattle and sheep at slaughter and from humans with yersiniosis in Great Britain during 1999-2000

Aims: To investigate the relationship between livestock carriage of Yersinia enterocolitica and human disease. The biotypes/serotypes of strains recovered from the faeces of pigs, cattle and sheep at slaughter during a national survey in Great Britain in 1999-2000, were compared with those of strains isolated from human cases of yersiniosis during the same period. Methods and Results: The faecal carriage of Y. enterocolitica by cattle, sheep and pigs at slaughter was 6.3, 10.7 and 26.1%, respectively. Yersinia enterocolitica biotype (BT) 1a was the most frequently isolated biotype from livestock (58%) and was the predominant biotype (53%) isolated from human cases over the same period. The main recognized pathogenic Y. enterocolitica biotype isolated from livestock was BT3 (O:5,27) (35% of sheep, 22% of pigs and 4% of cattle) but this biotype was not detected in any of the human isolates investigated. The major pathogenic biotypes of strains isolated from humans were BT3 (O:9) (24%) and BT4 (O:3) (19%) whereas of the veterinary isolates investigated, only pigs (11%) carried BT3 (O:9) strains. Conclusions: Because of significant overlaps in phenotypes of the veterinary and human strains it is not possible to comment on the correlation between host and pathogenicity, especially of biotype 1a. Significance and Impact of the Study: The data suggest that further investigations using methods with greater discriminatory power are required. However the data also suggests that pigs may be the primary reservoir for human pathogenic Y. enterocolitica infection

Photoassociation spectroscopy of cold calcium atoms

Photoassociation spectroscopy experiments on 40Ca atoms close to the dissociation limit 4s4s 1S0 - 4s4p 1P1 are presented. The vibronic spectrum was measured for detunings of the photoassociation laser ranging from 0.6 GHz to 68 GHz with respect to the atomic resonance. In contrast to previous measurements the rotational splitting of the vibrational lines was fully resolved. Full quantum mechanical numerical simulations of the photoassociation spectrum were performed which allowed us to put constraints on the possible range of the calcium scattering length to between 50 a_0 and 300 a_0

Depinning of a superfluid vortex line by Kelvin waves

We measure the interaction of a single superfluid vortex with surface irregularities. While vortex pinning in superconductors usually becomes weaker at higher temperatures, we find the opposite behavior. The pinning steadily increases throughout our measurement range, from 0.15Tc to over 0.5Tc. We also find that moving the other end of the vortex decreases the pinning, so we propose Kelvin waves along the vortex as a depinning mechanism.Comment: 5 figures; substantial revision including 2 new figure

Theoretical uncertainties for measurements of alpha_s from electroweak observables

One of the most precise measurements of the strong coupling constant alpha_s(MZ) is obtained in the context of global analyses of precision electroweak data. This article reviews the sensitivity of different electroweak observables to alpha_s and describes the perturbative uncertainties related to missing higher orders. The complete renormalisation scale dependence for the relevant observables is calculated at next-to-next-to-leading order and a new method is presented to determine the corresponding perturbative uncertainty for measurements of alpha_s based on these observables.Comment: v4: Revised version with new tables and figure

Refactoring smelly spreadsheet models

Identifying bad design patterns in software is a successful and inspiring research trend. While these patterns do not necessarily correspond to software errors, the fact is that they raise potential problematic issues, often referred to as code smells, and that can for example compromise maintainability or evolution. The identification of code smells in spreadsheets, which can be viewed as software development environments for non-professional programmers, has already been the subject of confluent researches by different groups. While these research groups have focused on detecting smells on concrete spreadsheets, or spreadsheet instances, in this paper we propose a comprehensive set of smells for abstract representations of spreadsheets, or spreadsheet models. We also propose a set of refactorings suggesting how spreadsheet models can become simpler to understand, manipulate and evolve. Finally we present the integration of both smells and refactorings under the MDSheet framework.Part funded by ERDF - European Regional Development Fund through the COMPETE Programme (operational programme for competitiveness) and by National Funds through the FCT - Fundação para a Ciência e a Tecnologia within projects FCOMP-01-0124-FEDER-022701 and Network Sensing for Critical Systems Monitoring (NORTE-01-0124-FEDER-000058), ref. BIM-2013 BestCase RL3.2 UMINHO

Effect of Phosphorus and Strontium Additions on Formation Temperature and Nucleation Density of Primary Silicon in Al-19 Wt Pct Si Alloy and Their Effect on Eutectic Temperature

The influence of P and Sr additions on the formation temperature and nucleation density of primary silicon in Al-19 wt pct Si alloy has been determined, for small volumes of melt solidified at cooling rates _T of ~0.3 and 1 K/s. The proportion of ingot featuring primary silicon decreased progressively with increased Sr addition, which also markedly reduced the temperature for first formation of primary silicon and the number of primary silicon particles per unit volume �Nv: When combined with previously published results, the effects of amount of P addition and cooling rate on �Nv are in reasonable accord with �Nv� _T ¼ ðp=6fÞ1=2 109 [250 � 215 (wt pct P)0.17]�3, where �Nv is in mm�3, _T is in K/s, and f is volume fraction of primary silicon. Increased P addition reduces the eutectic temperature, while increased Sr appears to generate a minimum in eutectic temperature at about 100 ppmw Sr

New evidence for strong nonthermal effects in Tycho's supernova remnant

For the case of Tycho's supernova remnant (SNR) we present the relation between the blast wave and contact discontinuity radii calculated within the nonlinear kinetic theory of cosmic ray (CR) acceleration in SNRs. It is demonstrated that these radii are confirmed by recently published Chandra measurements which show that the observed contact discontinuity radius is so close to the shock radius that it can only be explained by efficient CR acceleration which in turn makes the medium more compressible. Together with the recently determined new value $E_{sn}=1.2\times 10^{51}$ erg of the SN explosion energy this also confirms our previous conclusion that a TeV gamma-ray flux of $(2-5)\times 10^{-13}$ erg/(cm$^2$s) is to be expected from Tycho's SNR. Chandra measurements and the HEGRA upper limit of the TeV gamma-ray flux together limit the source distance $d$ to $3.3\leq d\leq 4$ kpc.Comment: 5 pages, 4 figures. Accepted for publication in Astrophysics and Space Science, Proc. of "The Multi-Messenger Approach to High-Energy Gamma-ray Sources (Third Workshop on the Nature of Unidentified High-Energy Sources)", Barcelona, July 4-7, 200