Throughout the biological and biomedical sciences there is a growing need for, prescriptive ‘minimum information’ (MI) checklists specifying the key information to include when reporting experimental results are beginning to find favor with experimentalists, analysts, publishers and funders alike. Such checklists aim to ensure that methods, data, analyses and results are described to a level sufficient to support the unambiguous interpretation, sophisticated search, reanalysis and experimental corroboration and reuse of data sets, facilitating the extraction of maximum value from data sets (...) them. However, such ‘minimum information’ MI checklists are usually developed independently by groups working within representatives of particular biologically- or technologically-delineated domains. Consequently, an overview of the full range of checklists can be difficult to establish without intensive searching, and even tracking thetheir individual evolution of single checklists may be a non-trivial exercise. Checklists are also inevitably partially redundant when measured one against another, and where they overlap is far from straightforward. Furthermore, conflicts in scope and arbitrary decisions on wording and sub-structuring make integration difficult. This presents inhibit their use in combination. Overall, these issues present significant difficulties for the users of checklists, especially those in areas such as systems biology, who routinely combine information from multiple biological domains and technology platforms. To address all of the above, we present MIBBI (Minimum Information for Biological and Biomedical Investigations); a web-based communal resource for such checklists, designed to act as a ‘one-stop shop’ for those exploring the range of extant checklist projects, and to foster collaborative, integrative development and ultimately promote gradual integration of checklists. (shrink)
Three experiments on neural grafting with adult rat hosts are described. Working memory impairments were produced by lesioning the hippocampus or severing its connections with the septum by ablating the fimbria-fornix. The results suggest that the survival and growth of a neural graft, whether an autograft or a xenograft, is not a necessary condition for functional recovery on a task tapping working memory.
Men and women report having significantly different numbers of sexual partners, which is impossible in a large sample. Schmitt's target article is no exception. This focuses discussion on the nature of the samples, their heterogeneity, and the locale they are drawn from. Further, we query how humans determine, for example, sex ratio, in the context of large numbers.
Variations in levels of apolipoprotein E have been tied to the risk and progression of Alzheimer's disease . Our group has previously compared and contrasted the promoters of the mouse and human ApoE gene promoter sequences and found notable similarities and significant differences that suggest the importance of the APOE promoter's role in the human disease. We examine here three specific single-nucleotide polymorphisms within the human APOE promoter region, specifically at -491 , -427 , and at -219 upstream from the (...) +1 transcription start site. The -219 and -491 polymorphic variations have significant association with instance of AD, and -491AA has significant risk even when stratified for the APOEepsilon4 allele. We also show significant effects on reporter gene expression in neuronal cell cultures, and, notably, these effects are modified by species origin of the cells. The -491 and -219 polymorphisms may have an interactive effect in addition to any independent activity. DNA-protein interactions differ between each polymorphic state. We propose SP1 and GATA as candidates for regulatory control of the -491 and -219 polymorphic sites. This work's significance lies in drawing connection among APOE promoter polymorphisms' associations with AD to functional promoter activity differences and specific changes in DNA-protein interactions in cell culture-based assays. Taken together, these results suggest that APOE expression levels are a risk factor for AD irrespective of APOEepsilon4 allele status. (shrink)
This article was written as a commentary on a target article by Peter W. Ross entitled "The Location Problem for Color Subjectivism" [Consciousness and Cognition 10(1), 42-58 (2001)], and is published together with it, and with other commentaries and Ross's reply. If you or your library have the necessary subscription you can get PDF versions of the target article, all the commentaries, and Ross's reply to the commentaries here. However, I do not think that it is by any means essential (...) for you to have read Ross's piece in order to understand this one. Ross defends a view called "color physicalism" or color realism that holds (simplifying somewhat) that colors are real physical properties (in typical cases, spectral reflectances of object surfaces). This is in opposition to what is probably a more widely held "subjectivist" view of color, holding that color qualities really exist only in the mind. In my commentary I suggest that a realist view of qualitative properties, such as Ross's, together with a direct, active view of perception, and a concept of "extended mind" (Clark & Chalmers, 1998) may provide the materials for a real solution to the notorious hard problem of consciousness. I sketch this solution in outline. - N.J.T.T. (shrink)