The DUB/USP17 deubiquitinating enzymes, a multigene family within a tandemly repeated sequence

Here we report the identification of 10 human, 1 murine, and 2 rat ORFs, all of which represent additional members of the DUB/USP17 family of deubiquitinating enzymes. In addition, we demonstrate that this family constitutes part of a tandemly repeated sequence conserved throughout humans, mice, and rats. Furthermore, upon examination of the known family members we have found that the multiple genes observed, in contrast to other gene families, have arisen due to the independent expansion of an ancestral sequence within each species. This premise is further strengthened by the observation that the murine and rat genes span two exons while their human counterparts have one. These observations, in conjunction with previous work demonstrating that the DUB/USP17's are cytokine inducible and that they regulate both cell growth and survival, suggest that the DUB/USP17's are a large highly conserved family of genes that may play an important role in controlling cell fate.

The mouse and human IGSF6 (DORA) genes map to the inflammatory bowel disease 1 locus and are embedded in an intron of a gene of unknown function.

We have previously characterized IGSF6 (DORA), a novel member of the immunoglobulin superfamily (IGSF) from human and rat expressed in dendritic and myeloid cells. Using a probe from the open reading frame of the rat cDNA, we isolated a cosmid which contains the entire mouse gene. By comparative analysis and reverse transcriptase polymerase chain reaction, we defined the intron/exon structure and the mRNA of the mouse gene and, with respect to human BAC clones, the human gene. The genes span 10 kb (mouse) and 12 kb (human), with six exons arranged in a manner similar to other members of the IGSF. All intron/exon boundaries follow the GT-AG rule. Expression of the mouse Igsf6 gene is restricted to cells of the immune system, particularly macrophages. Northern blot revealed a single mRNA of 2.5 kb, in contrast to the human gene which is expressed as two mRNAs of 1 and 2.5 kb. The human and mouse genes were localized to a locus associated with inflammatory bowel disease. Analysis of the flanking regions of the Igsf6 gene revealed the presence of an unrelated gene, transcribed from the opposite strand of the DNA and oriented such that the Igsf6 gene is encoded entirely within an intron. An identical organization is seen in human. This gene of unknown function is transcribed and processed, contains homologues in Caenorhabditis elegans and prokaryotes, and is expressed in most organs in the mouse.

Application of static charge transfer within an ionic-liquid force field and its effect on structure and dynamics

The effects of linear scaling of the atomic charges of a reference potential on the structure, dynamics, and energetics of the ionic liquid 1,3-dimethylimidazolium chloride are investigated. Diffusion coefficients that span over four orders of magnitude are observed between the original model and a scaled model in which the ionic charges are +/- 0.5 e. While the three-dimensional structure of the liquid is less affected, the partial radial distribution functions change markedly-with the positive result that for ionic charges of +/- 0.7 e, an excellent agreement is observed with ab initio molecular dynamics data. Cohesive energy densities calculated from these partial-charge models are also in better agreement with those calculated from the ab initio data. We postulate that ionic-liquid models in which the ionic charges are assumed to be +/- 1 e overestimate the intermolecular attractions between ions, which results in overstructuring, slow dynamics, and increased cohesive energy densities. The use of scaled-charge sets may be of benefit in the simulation of these systems-especially when looking at properties beyond liquid structure-thus providing on alternative to computationally expensive polarisable force fields.

Trends in C-O and C-N bond formations over transition metal surfaces: An insight into kinetic sensitivity in catalytic reactions

Transition metal catalyzed bond formation is a fundamental process in catalysis and is of general interest throughout chemistry. To date, however, the knowledge of association reactions is rather limited, relative to what is known about dissociative processes. For example, surprisingly little is known about how the bond-forming ability of a metal, in general, varies across the Periodic Table. In particular, the effect of reactant valency on such trends is poorly understood. Herein, the authors examine these key issues by using density functional theory calculations to study CO and CN formations over the 4d metals. The calculations reveal that the chemistries differ in a fundamental way. In the case of CO formation, the reaction enthalpies span a much greater range than those of CN formation. Moreover, CO formation is found to be kinetically sensitive to the metal; here the reaction barriers (E-a) are found to be influenced by the reaction enthalpy. CN formation, conversely, is found to be relatively kinetically insensitive to the metal, and there is no correlation found between the reaction barriers and the reaction enthalpy. Analysis has shown that at the final adsorbed state, the interaction between N and the surface is relatively greater than that of O. Furthermore, in comparison with O, relatively less bonding between the surface and N is observed to be lost during transition state formation. These greater interactions between N and the surface, which can be related to the larger valency of N, are found to be responsible for the relatively smaller enthalpy range and limited variation in E-a for CN formation. (C) 2007 American Institute of Physics.

Ten Year Performance Evaluation of a Field-Scale Zero-Valent Iron Permeable Reactive Barrier Installed to Remediate Trichloroethene Contaminated Groundwater

The Monkstown Fe0 PRB, Europe’s oldest commercially installed PRB, had been treating trichloroethene (TCE) contaminated groundwater for about 10 years on the Nortel Network site in Northern Ireland when cores were collected in December, 2006. Groundwater data from 2001-2006 indicated that TCE is being remediated to below detection limits as the contaminated groundwater flows through the PRB, Ca and Fe carbonates, crystalline and amorphous FeS, and Fe (oxy)hydroxides precipitates are present in the Fe0 filing material within the PRB. A greater variety of minerals are associated with a 1 cm thick slightly cemented crust at the entrance of the Fe0 section of the reactive vessel and the discontinuous cemented Fe0 material directly below it. Also, a greater presence of microbial communities occurred in the upper portion of the PRB compared to the lower section which might be due to less favourable conditions (i.e. high pH, low oxygen) for microbial growth in the lower section of the PRB. Visual estimation suggests that the Fe0 filings in the effluent section of the PRB have life-span of 10+ years compared to the Fe0 filings in the thin influent section of the PRB which may have a life span of only ~2-5 more years. Multi-tracer tests indicated that preferential pathways have formed in this PRB over the 10 years of operation.

A 4500-year proxy climate record from peatlands in the North of Ireland: the identification of widespread summer ‘drought phases’?

Mid-to-late Holocene high-resolution testate amoebae-derived water table reconstructions from two peatlands in the North of Ireland are presented. The proxy climate records are dated and correlated using a combination of AMS 14C dating, spheroidal carbonaceous particles and tephrochronology. The reconstructions start prior to the Hekla 4 tephra isochron (2395–2279 BC) and thus span the last ~4500 years. The records are compiled by the process of tuning within chronological errors, standardisation and stacking. Comparisons are made to existing palaeoclimate records from peatlands in Northern Britain and Ireland and the compiled lake-level record for mid-latitude Europe. Four coherent dry phases are identified in the records at ca 1150–800 BC, 320 BC–AD 150, AD 250–470 and AD 1850–2000. Recent research has shown that peat-derived water table reconstructions reflect summer water deficit and therefore the dry phases are interpreted as periods with a higher frequency and/or greater magnitudes of summer drought. These ‘drought phases’ occur during periods of relatively low 14C production, which may add support to the hypothesis of persistent solar forcing of climate change during the Holocene. Any relationship with the North Atlantic stacked drift ice record is less clear. © 2009 Elsevier Ltd. All rights reserved.

Effect of corrosion of reinforcement on the mechanical behaviour of highly corroded RC beams

This paper describes an experimental investigation of the behaviour of corroded reinforced concrete beams. These have been stored in a chloride environment for a period of 26 years under service loading so as to be representative of real structural and environmental conditions. The configuration and the widths of the cracks in the two seriously corroded short-span beams were depicted carefully, and then the beams were tested until failure by a three-point loading system. Another two beams of the same age but without corrosion were also tested as control specimens. A short span arrangement was chosen to investigate any effect of a reduction in the area and bond strength of the reinforcement on shear capacity. The relationship of load and deflection was recorded so as to better understand the mechanical behaviour of the corroded beams, together with the slip of the tensile bars. The corrosion maps and the loss of area of the tensile bars were also described after having extracted the corroded bars from the concrete beams. Tensile tests of the main longitudinal bars were also carried out. The residual mechanical behaviour of the beams is discussed in terms of the experimental results and the cracking maps. The results show that the corrosion of the reinforcement in the beams induced by chloride has a very important effect on the mechanical behaviour of the short-span beams, as loss of cross-sectional area and bond strength have a very significant effect on the bending capacity.

Novel loading tests on full-scale tapered member portal frames

This paper presents the experimental results of loading tests on two 18m span tapered member portal frames designed to BS 5950. Deflection test results for vertical, lateral and combined loading cases are compared with the predictions given by elastic analysis to BS 5950 and shown to be favourable. The predicted ultimate capacities and modes of failure, which were by lateral-torsional buckling of the columns, were also found to agree with the experimental behaviour. It was found that the method of modelling the tapered members as a series of prismatic elements gave good comparison with test results.

Finite element investigation of the structural behaviour of deck slabs in composite bridges

This research studies the structural behaviour of bridge deck slabs under static patch loads in steel–concrete composite bridges and investigates compressive membrane action (CMA) in concrete bridge decks slabs, which governs the structural behaviour. A non-linear 3D finite element analysis models was developed using ABAQUS 6.5 software packages. Experimental data from one-span composite bridge structures are used to validate and calibrate the proposed FEM models. A series of parametric studies is conducted. The analysis results are discussed and conclusions on the behaviour of the bridge decks are presented.

Cue Competition Effects and Young Children's Causal and Counterfactual Inferences

The authors examined cue competition effects in young children using the blicket detector paradigm, in which objects are placed either singly or in pairs on a novel machine and children must judge which objects have the causal power to make the machine work. Cue competition effects were found in a 5- to 6-year-old group but not in a 4-year-old group. Equivalent levels of forward and backward blocking were found in the former group. Children's counterfactual judgments were subsequently examined by asking whether or not the machine would have gone off in the absence of I of 2 objects that had been placed on it as a pair. Cue competition effects were demonstrated only in 5- to 6-year-olds using this mode of assessing causal reasoning.

An Assessment of Sheltered Housing Design in Belfast, Northern Ireland

This article presents a UK-based research that has studied the existing sheltered or assisted living housing population and its future housing options and preferences. This meets an identified need to know and understand users' needs and requirements in much more detail that outlines what is liked and disliked by older people about sheltered housing, so that those who plan and design such housing can be aware of their views. The study also sought to understand the architects' challenges in designing and adapting this type of housing. The sheltered housing managed by housing associations in Belfast, Northern Ireland, was assessed through a series of site visits, structured interviews, and a focus group with stakeholders. Findings revealed older users' keen interest in participating in their housing needs assessment, identified building design concerns and provided recommendations for potential design guidelines. The findings of this research have provided important policy and design guidance to NI housing providers, and also allowed various stakeholders to participate in the debate about the quality of housing provided for the older people. This is a significant research study that generated considerable interest from various housing providers. This is an international peer reviewed journal.

Controllable Gaussian-Qubit Interface for Extremal Quantum State Engineering

We study state engineering through bilinear interactions between two remote qubits and two-mode Gaussian light fields. The attainable two-qubit states span the entire physically allowed region in the entanglement-versus-global-purity plane. Two-mode Gaussian states with maximal entanglement at fixed global and marginal entropies produce maximally entangled two-qubit states in the corresponding entropic diagram. We show that a small set of parameters characterizing extremally entangled two-mode Gaussian states is sufficient to control the engineering of extremally entangled two-qubit states, which can be realized in realistic matter-light scenarios.

An investigation into the behaviour of concrete containing seawater-neutralised bauxite refinery residues in silage effluent

The farm production of silage as a winter-feed supplement is widespread. However, the bins in which silage is produced are subject to acidic and microbial attacks. Both these types of attack can lead to a weakening and failure of the concretes, especially on the outer lip of the open side of the silage pit. Consequently, the development of an acid-resistant concrete that can extend the life span of silage bins on farms could lead to considerable cost savings for farmers and, hence, can improve farm productivity. This paper reports on test results of an investigation into the behaviour of concrete containing seawater-neutralised bauxite refinery residues (Bauxsol™) exposed to sulphuric acid environments in the laboratory and to silage effluents. The concrete manufactured had a fixed water–cement ratio of 0.55 and natural sand was replaced with the Bauxsol™ at 0%, 5%, 10%, 15% and 20% by cement mass. Results indicated that the use of Bauxsol™ as a sand replacement material improved the behaviour of concrete both in sulphuric acid in the laboratory as well as in the silage effluent. Consequently, it is concluded that the Bauxsol™ can be used to replace 10% of natural sand to produce concrete that is resistant to silage effluents, providing an extended service life over conventional concretes used in silage pits.

Ascertaining the perspectives of young children in care: case studies using reality boxes

This article describes the use of an innovative method, reality boxes, to elicit the perspectives of children, ages four to seven years, in state care. Using examples from a broader research project based on children in Northern Ireland, which was concerned with their participation rights, the article considers how the children used the boxes to express their views. Informed by a child rights-based approach, the article highlights the processes and practices involved and concludes by stressing the potential importance of this method, used in the context of this framework, in social work practice with young children.