Gene Sequence and the 1.8 Å Crystal Structure of the Tungsten-Containing Formate Dehydrogenase from Desulfovibrio gigas

AbstractDesulfovibrio gigas formate dehydrogenase is the first representative of a tungsten-containing enzyme from a mesophile that has been structurally characterized. It is a heterodimer of 110 and 24 kDa subunits. The large subunit, homologous to E. coli FDH-H and to D. desulfuricans nitrate reductase, harbors the W site and one [4Fe-4S] center. No small subunit ortholog containing three [4Fe-4S] clusters has been reported. The structural homology with E. coli FDH-H shows that the essential residues (SeCys158, His159, and Arg407) at the active site are conserved. The active site is accessible via a positively charged tunnel, while product release may be facilitated, for H+ by buried waters and protonable amino acids and for CO2 through a hydrophobic channel

Quantification of different iron forms in the aceruloplasminemia brain to explore iron-related neurodegeneration

Biological and Soft Matter Physic

How to keep it adequate: A protocol for ensuring validity in agent-based simulation

There has so far been no shared understanding of validity in agent-based simulation. We here conceptualise validation as systematically substantiating the premises on which conclusions from simulation analysis for a particular modelling context are built. Given such a systematic perspective, validity of agent-based models cannot be ensured if validation is merely understood as an isolated step in the modelling process. Rather, valid conclusions from simulation analysis require context-adequate method choices at all steps of the simulation analysis including model construction, model and parameter inference, uncertainty analysis and simulation. We present a twelve-step protocol to highlight the (often hidden) premises for methodological choices and their link to the modelling context. It is designed to aid modelers in understanding their context and in choosing and documenting context-adequate and mutually consistent methods throughout the modelling process. Its purpose is to assist reviewers and the community as a whole in assessing and discussing context-adequacy

Resummation of the hadronic tau decay width with the modified Borel transform method

A modified Borel transform of the Adler function is used to resum the hadronic tau decay width ratio. In contrast to the ordinary Borel transform, the integrand of the Borel integral is renormalization--scale invariant. We use an ansatz which explicitly accounts for the structure of the leading infrared renormalon. Further, we use judiciously chosen conformal transformations for the Borel variable, in order to map sufficiently away from the origin the other ultraviolet and infrared renormalon singularities. In addition, we apply Pade approximants for the corresponding truncated perturbation series of the modified Borel transform, in order to further accelerate the convergence. Comparing the results with the presently available experimental data on the tau hadronic decay width ratio, we obtain $\alpha_s(M^z) = 0.1192 +- 0.0007_{exp.} +- 0.0010_{EW+CKM} +- 0.0009_{th.} +- 0.0003_{evol.}$. These predictions virtually agree with those of our previous resummations where we used ordinary Borel transforms instead.Comment: 32 pages, 2 eps-figures, revtex; minor changes in the formulations; a typo in Eq.(47) corrected; version as appearing in Phys. Rev.

Habitat use by the endangered white-clawed crayfish Austropotamobius species complex: a systematic review

Understanding habitat requirements is a key part of conserving declining species, particularly when reintroductions are planned as part of the recovery strategy. The white-clawed crayfish (Austropotamobius pallipes) has undergone severe declines across its range and is now classified by the International Union for Conservation of Nature (IUCN) as ‘endangered’. Translocation of threatened A. pallipes populations to isolated ‘Ark sites’ where threats are minimised is an increasingly used conservation tool. A full feasibility assessment of potential Ark sites, including an assessment of habitat suitability, is recommended within translocation guidelines developed by the IUCN. This literature review employed a systematic search and ‘vote counting’ approach to identify and assess the relative importance of physical habitat requirements of A. pallipes. Many habitat features were positively associated with crayfish presence, in particular: boulder substrate, trees/shading, woody debris, exposed roots, and undercut banks; and habitat use patterns varied among crayfish sexes and size classes. Ark sites should incorporate heterogeneous habitat, with as many of these features as possible, to provide both ample refugia and rich foraging areas

Search for charginos in e+e- interactions at sqrt(s) = 189 GeV

An update of the searches for charginos and gravitinos is presented, based on a data sample corresponding to the 158 pb^{-1} recorded by the DELPHI detector in 1998, at a centre-of-mass energy of 189 GeV. No evidence for a signal was found. The lower mass limits are 4-5 GeV/c^2 higher than those obtained at a centre-of-mass energy of 183 GeV. The (\mu,M_2) MSSM domain excluded by combining the chargino searches with neutralino searches at the Z resonance implies a limit on the mass of the lightest neutralino which, for a heavy sneutrino, is constrained to be above 31.0 GeV/c^2 for tan(beta) \geq 1.Comment: 22 pages, 8 figure

Hadronization properties of b quarks compared to light quarks in e+e- -> q qbar from 183 to 200 GeV

The DELPHI detector at LEP has collected 54 pb^{-1} of data at a centre-of-mass energy around 183 GeV during 1997, 158 pb^{-1} around 189 GeV during 1998, and 187 pb^{-1} between 192 and 200 GeV during 1999. These data were used to measure the average charged particle multiplicity in e+e- -> b bbar events, _{bb}, and the difference delta_{bl} between _{bb} and the multiplicity, _{ll}, in generic light quark (u,d,s) events: delta_{bl}(183 GeV) = 4.55 +/- 1.31 (stat) +/- 0.73 (syst) delta_{bl}(189 GeV) = 4.43 +/- 0.85 (stat) +/- 0.61 (syst) delta_{bl}(200 GeV) = 3.39 +/- 0.89 (stat) +/- 1.01 (syst). This result is consistent with QCD predictions, while it is inconsistent with calculations assuming that the multiplicity accompanying the decay of a heavy quark is independent of the mass of the quark itself.Comment: 13 pages, 2 figure