influence.ME: tools for detecting influential data in mixed effects models

influence.ME provides tools for detecting influential data in mixed effects models. The application of these models has become common practice, but the development of diagnostic tools has lagged behind. influence.ME calculates standardized measures of influential data for the point estimates of generalized mixed effects models, such as DFBETAS, Cook’s distance, as well as percentile change and a test for changing levels of significance. influence.ME calculates these measures of influence while accounting for the nesting structure of the data. The package and measures of influential data\ud are introduced, a practical example is given, and strategies for dealing with influential data are suggested

A Comparison between Relativistic and Semi-Relativistic Treatment in the Diquark-Quark Model

In the diquark-quark model of the nucleon including scalar and axialvector diquarks we compare solutions of the ladder Bethe-Salpeter equation in the instantaneous Salpeter approximation and in the fully covariant (i.e. four-dimensional) treatment. We obtain that the binding energy is severly underestimated in the Salpeter approximation. For the electromagnetic form factors of the nucleon we find that in both approaches the overall shapes of the respective form factors are reasonably similar up to $Q^2 \approx 0.4$ GeV^2. However, the magnetic moments differ substantially as well as results for the pion-nucleon and the axial coupling of the nucleon.Comment: 12 pages,4 figures, 3 tables; minor modifications in text and tables, references added, version to be published in Physics Letters

Integrated Timber Allocation and Transportation Planning in Ireland

Coillte Teoranta, the Irish Forestry Board, was established as a forestry company in 1989, with a mandate to operate in forestry and related activities in a commercial manner. The company took over the assets of the state Forest Service and now owns and manages approximately 400,000 ha of forest. Coillte harvests and sells timber to the private wood processing industries in Ireland. Coillte harvested approximately 1.4 million m3 of timber in 1990. By 2010 this annual harvest volume will increase to 3.5 million m3. In order to manage the harvesting and transportation operations efficiently, a national timber sales allocation procedure was developed by the Forestry Department of University College, Dublin. The procedure uses Coillte's databases on harvest volumes, subdivided into supply categories; on mill demands, specified by demand categories; and on the national transportation network, including road, rail and water transport modes. The developed operational procedure was used as a decision-making tool during the allocation of the 1991 sales volumes. A comparison of the actual versus the optimized 1990 allocation strategy identified opportunities for large-scale savings. In addition to its main function as a decision-making tool for the annual sales allocation, the model has been used for other strategic and tactical planning analyses, such as the influence of new mill location on transport costs, the impacts of a timber processing industry rationalization programme on the industry as a whole and on individual mills, the feasibility of timber transport by rail, the selection of suitable ports for timber export, and the impact of road construction and improvement programmes on national timber transport strategies. The model has been successfully linked with the company's ARC/ INFO Geographic Information System which extends the post-allocation analysis and interpretation capabilities, and combines the output with existing information systems. A further integration of the procedure in the management decision-making processes in the company will result in increased cost saving opportunities

Reply: Evaluation of management of desmoid tumours associated with familial adenomatous polyposis in Dutch patients

Cellular mechanisms in basic and clinical gastroenterology and hepatolog

Extensive Association of Common Disease Variants with Regulatory Sequence

Overlap between non-coding DNA regulatory sequences and common variant associations can help to identify specific cell and tissue types that are relevant for particular diseases. In a systematic manner, we analyzed variants from 94 genome-wide association studies (reporting at least 12 loci at p<5x10-8) by projecting them onto 466 epigenetic datasets (characterizing DNase I hypersensitive sites; DHSs) derived from various adult and fetal tissue samples and cell lines including many biological replicates. We were able to confirm many expected associations, such as the involvement of specific immune cell types in immune-related diseases and tissue types in diseases that affect specific organs, for example, inflammatory bowel disease and coronary artery disease. Other notable associations include adrenal glands in coronary artery disease, the immune system in Alzheimer's disease, and the kidney for bone marrow density. The association signals for some GWAS (for example, myopia or age at menarche) did not show a clear pattern with any of the cell or tissue types studied. In general, the identified variants from GWAS tend to be located outside coding regions. Altogether, we have performed an extensive characterization of GWAS signals in relation to cell and tissue-specific DHSs, demonstrating a key role for regulatory mechanisms in common diseases and complex traits