Development of a pilot data management infrastructure for biomedical researchers at University of Manchester – approach, findings, challenges and outlook of the MaDAM Project

Management and curation of digital data has been becoming ever more important in a higher education and research environment characterised by large and complex data, demand for more interdisciplinary and collaborative work, extended funder requirements and use of e-infrastructures to facilitate new research methods and paradigms. This paper presents the approach, technical infrastructure, findings, challenges and outlook (including future development within the successor project, MiSS) of the ‘MaDAM: Pilot data management infrastructure for biomedical researchers at University of Manchester’ project funded under the infrastructure strand of the JISC Managing Research Data (JISCMRD) programme. MaDAM developed a pilot research data management solution at the University of Manchester based on biomedical researchers’ requirements, which includes technical and governance components with the flexibility to meet future needs across multiple research groups and disciplines

High-temperature series for the bond-diluted Ising model in 3, 4 and 5 dimensions

In order to study the influence of quenched disorder on second-order phase transitions, high-temperature series expansions of the \sus and the free energy are obtained for the quenched bond-diluted Ising model in $d = 3$--5 dimensions. They are analysed using different extrapolation methods tailored to the expected singularity behaviours. In $d = 4$ and 5 dimensions we confirm that the critical behaviour is governed by the pure fixed point up to dilutions near the geometric bond percolation threshold. The existence and form of logarithmic corrections for the pure Ising model in $d = 4$ is confirmed and our results for the critical behaviour of the diluted system are in agreement with the type of singularity predicted by renormalization group considerations. In three dimensions we find large crossover effects between the pure Ising, percolation and random fixed point. We estimate the critical exponent of the \sus to be $\gamma =1.305(5)$ at the random fixed point.Comment: 16 pages, 10 figure

Interaction dependence of composite fermion effective masses

We estimate the composite fermion effective mass for a general two particle potential r^{-\alpha} using exact diagonalization for polarized electrons in the lowest Landau level on a sphere. Our data for the ground state energy at filling fraction \nu=1/2 as well as estimates of the excitation gap at \nu=1/3, 2/5 and 3/7 show that m_eff \sim \alpha^{-1}.Comment: 4 pages, RevTeX, 5 figure

Unpolarized quasielectrons and the spin polarization at filling fractions between 1/3 and 2/5

We prove that for a hard core interaction the ground state spin polarization in the low Zeeman energy limit is given by $P=2/\nu-5$ for filling fractions in the range $1/3 \leq\nu\leq 2/5$. The same result holds for a Coulomb potential except for marginally small magnetic fields. At the magnetic fields $B<20T$ unpolarized quasielectrons can manifest themselves by a characteristic peak in the I-V characteristics for tunneling between two $\nu=1/3$ ferromagnets.Comment: 8 pages, Latex. accepted for publication in Phys.Rev.

Chagas Disease: Detection of Trypanosoma cruzi by a New, High-Specific Real Time PCR

Background: Chagas disease (CD) is a major burden in Latin America, expanding also to non-endemic countries. A gold standard to detect the CD causing pathogen Trypanosoma cruzi is currently not available. Existing real time polymerase chain reactions (RT-PCRs) lack sensitivity and/or specificity. We present a new, highly specific RT-PCR for the diagnosis and monitoring of CD. Material and Methods: We analyzed 352 serum samples from Indigenous people living in high endemic CD areas of Colombia using three leading RT-PCRs (k-DNA-, TCZ-, 18S rRNA-PCR), the newly developed one (NDO-PCR), a Rapid Test/enzyme-linked immuno sorbent assay (ELISA), and immunofluorescence. Eighty-seven PCR-products were verified by sequence analysis after plasmid vector preparation. Results: The NDO-PCR showed the highest sensitivity (92.3%), specificity (100%), and accuracy (94.3%) for T. cruzi detection in the 87 sequenced samples. Sensitivities and specificities of the kDNA-PCR were 89.2%/22.7%, 20.5%/100% for TCZ-PCR, and 1.5%/100% for the 18S rRNA-PCR. The kDNA-PCR revealed a 77.3% false positive rate, mostly due to cross-reactions with T. rangeli (NDO-PCR 0%). TCZ- and 18S rRNA-PCR showed a false negative rate of 79.5% and 98.5% (NDO-PCR 7.7%), respectively. Conclusions: The NDO-PCR demonstrated the highest specificity, sensitivity, and accuracy compared to leading PCRs. Together with serologic tests, it can be considered as a reliable tool for CD detection and can improve CD management significantly

Star-graph expansions for bond-diluted Potts models

We derive high-temperature series expansions for the free energy and the susceptibility of random-bond $q$-state Potts models on hypercubic lattices using a star-graph expansion technique. This method enables the exact calculation of quenched disorder averages for arbitrary uncorrelated coupling distributions. Moreover, we can keep the disorder strength $p$ as well as the dimension $d$ as symbolic parameters. By applying several series analysis techniques to the new series expansions, one can scan large regions of the $(p,d)$ parameter space for any value of $q$. For the bond-diluted 4-state Potts model in three dimensions, which exhibits a rather strong first-order phase transition in the undiluted case, we present results for the transition temperature and the effective critical exponent $\gamma$ as a function of $p$ as obtained from the analysis of susceptibility series up to order 18. A comparison with recent Monte Carlo data (Chatelain {\em et al.}, Phys. Rev. E64, 036120(2001)) shows signals for the softening to a second-order transition at finite disorder strength.Comment: 8 pages, 6 figure

Static solitons with non-zero Hopf number

We investigate a generalized non-linear O(3) $\sigma$-model in three space dimensions where the fields are maps $S^3 \mapsto S^2$. Such maps are classified by a homotopy invariant called the Hopf number which takes integer values. The model exhibits soliton solutions of closed vortex type which have a lower topological bound on their energies. We explicitly compute the fields for topological charge 1 and 2 and discuss their shapes and binding energies. The effect of an additional potential term is considered and an approximation is given for the spectrum of slowly rotating solitons.Comment: 13 pages, RevTeX, 7 Postscript figures, minor changes have been made, a reference has been corrected and a figure replace

Sphaleron Effects Near the Critical Temperature

We discuss one-loop radiative corrections to the sphaleron-induced baryon number-violating transition rate near the electroweak phase transition in the standard model. We emphasize that in the case of a first-order transition a rearrangement of the loop expansion is required close to the transition temperature. The corresponding expansion parameter, the effective 3-dimensional gauge coupling approaches a finite $\lambda$ dependent value at the critical temperature. The $\lambda$ (Higgs mass) dependence of the 1-loop radiative corrections is discussed in the framework of the heat kernel method. Radiative corrections are small compared to the leading sphaleron contribution as long as the Higgs mass is small compared to the W mass. To 1-loop accuracy, there is no Higgs mass range compatible with experimental limits where washing-out of a B+L asymmetry could be avoided for the minimal standard model with one Higgs doublet.Comment: 17 pages, RevTeX, (4 figures in a separate uuencoded file), HD-THEP-93-23re

XCR1 expression distinguishes human conventional dendritic cell type 1 with full effector functions from their immediate precursors

Dendritic cells (DCs) are major regulators of innate and adaptive immune responses. DCs can be classified into plasmacytoid DCs and conventional DCs (cDCs) type 1 and 2. Murine and human cDC1 share the mRNA expression of XCR1. Murine studies indicated a specific role of the XCR1-XCL1 axis in the induction of immune responses. Here, we describe that human cDC1 can be distinguished into XCR1$^{-}$ and XCR1$^{+}$ cDC1 in lymphoid as well as nonlymphoid tissues. Steady-state XCR1$^{+}$ cDC1 display a preactivated phenotype compared to XCR1$^{-}$ cDC1. Upon stimulation, XCR1$^{+}$ cDC1, but not XCR1$^{-}$ cDC1, secreted high levels of inflammatory cytokines as well as chemokines. This was associated with enhanced activation of NK cells mediated by XCR1$^{+}$ cDC1. Moreover, XCR1$^{+}$ cDC1 excelled in inhibiting replication of Influenza A virus. Further, under DC differentiation conditions, XCR1$^{-}$ cDC1 developed into XCR1$^{+}$ cDC1. After acquisition of XCR1 expression, XCR1$^{-}$ cDC1 secreted comparable level of inflammatory cytokines. Thus, XCR1 is a marker of terminally differentiated cDC1 that licenses the antiviral effector functions of human cDC1, while XCR1$^{-}$ cDC1 seem to represent a late immediate precursor of cDC1

Genetic characterization of Yug Bogdanovac virus

We present pyrosequencing data and phylogenetic analysis for the full genome of Yug Bogdanovac virus (YBV), a member of the Vesicular stomatitis virus serogroup of the Rhabdoviridae isolated from a pool of Phlebotomus perfiliewi sandflies collected in Serbia in 1976. YBV shows very low nucleotide identities to other members of the Vesicular stomatitis virus serogroup and does not contain a reading frame for C&prime;/C proteins