The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models.

MOTIVATION: Molecular biotechnology now makes it possible to build elaborate systems models, but the systems biology community needs information standards if models are to be shared, evaluated and developed cooperatively. RESULTS: We summarize the Systems Biology Markup Language (SBML) Level 1, a free, open, XML-based format for representing biochemical reaction networks. SBML is a software-independent language for describing models common to research in many areas of computational biology, including cell signaling pathways, metabolic pathways, gene regulation, and others. AVAILABILITY: The specification of SBML Level 1 is freely available from http://www.sbml.org/

pathSCOUT: exploration and analysis of biochemical pathways.

UNLABELLED: pathSCOUT provides access, display and exploration of data relevant to biochemical pathways, and enables analysis of pathway model structure and behavior. AVAILABILITY: pathSCOUT is available as a customized solution from contact@lionbioscience.com; limited evaluation access and additional information is available from http://simpath.lionbioscience.com:8080/documents/pathscout11/.

[Geographic distribution maps of human genes in China].

The first set of geographic distribution maps of human gene in China are published, including 12 alleles: IB and IO of ABO system, m of MNS system, P1, Rh-D, A1 and A11 of HLA system, Gm1;21 and Gm1,3;5 of immunoglobulin, AK1, deficient type of G6PD, and PTC test blindness gene t. These maps not only show the geographic distribution of alleles, but also can be used to study the origin and dispersal of some alleles, gene flow, and the effect of some selective factors on gene frequencies.

The Rosetta Stone of stability.

A number of proposals to augment the classical theory of natural selection turn on the need to consider the role of neutral genetic modifications, as well as on the role of patterns of physicochemically stable substructures. There are similarities between this opposition and that within cognitive science, where the dynamic and computational approaches emphasize complementary aspects of perceptual-motor development. This paper summarizes the relevant arguments of the various schools of evolutionary and cognitive theory, as well as the various calls that have been made for unification or complementarity of explanations. An extended concept of stability is then proposed, which bridges the gap between thermodynamic equilibrium and semantic closure.

Further characteristics of proto-European y chromosomes.

We examined a set of populations mainly from Europe but also from the Middle East and North Africa for the three Y-linked microsatellites YCAII, DYS19 (about 1300 individuals) and DYS392 (about 350 individuals). Three markers (YCAII a5-b1 Ht, DYS19-190 bp and DYS392-254 bp) show decreasing gradients of frequency from western Europe towards the Middle East which parallel that of the proto-European 49a,f/TaqI Ht 15. Indeed, a strong linkage disequilibrium between these markers and the 49a,f Ht15 is observed. We therefore suggest that the 49a,f/TaqI Ht15, YCAII a5-b1 Ht, DYS19-190 bp and DYS392-254 bp Y chromosome could represent a component of the proto-European gene pool. This European specific compound haplotype distinctively characterises western Europeans and its very high incidence in these populations (particularly in the Basques) is discussed.

Genetic evidence for a higher female migration rate in humans.

Mitochondrial DNA and the Y chromosome have been used extensively in the study of modern human origins and other phylogenetic questions, but not in the context of their sex-specific modes of transmission. mtDNA is transmitted exclusively by females, whereas the Y chromosome is passed only among males. As a result, differences in the reproductive output or migration rate of males and females will influence the geographic patterns and relative level of genetic diversity on the Y chromosome, autosomes and mtDNA (ref. 1). We have found that Y chromosome variants tend to be more localized geographically than those of mtDNA and the autosomes. The fraction of variation within human populations for Y chromosome single nucleotide polymorphisms (SNPs) is 35.5%, versus 80-85% for the autosomes and mtDNA (refs 6-8). A higher female than male migration rate (via patrilocality, the tendency for a wife to move into her husband's natal household) explains most of this discrepancy, because diverse Y chromosomes would enter a population at a lower rate than mtDNA or the autosomes. Polygyny may also contribute, but the reduction of variation within populations that we measure for the Y chromosome, relative to the autosomes and mitochondrial DNA, is of such magnitude that differences in the effective population sizes of the sexes alone are insufficient to produce the observation.

An apportionment of human DNA diversity.

It is often taken for granted that the human species is divided in rather homogeneous groups or races, among which biological differences are large. Studies of allele frequencies do not support this view, but they have not been sufficient to rule it out either. We analyzed human molecular diversity at 109 DNA markers, namely 30 microsatellite loci and 79 polymorphic restriction sites (restriction fragment length polymorphism loci) in 16 populations of the world. By partitioning genetic variances at three hierarchical levels of population subdivision, we found that differences between members of the same population account for 84.4% of the total, which is in excellent agreement with estimates based on allele frequencies of classic, protein polymorphisms. Genetic variation remains high even within small population groups. On the average, microsatellite and restriction fragment length polymorphism loci yield identical estimates. Differences among continents represent roughly 1/10 of human molecular diversity, which does not suggest that the racial subdivision of our species reflects any major discontinuity in our genome.

Genetics and the origin of European languages.

A new set of European genetic data has been analyzed to dissect independent patterns of geographic variation. The most important cause of European genetic variation has been confirmed to correspond to the migration of Neolithic farmers from the area of origin of agriculture in the Middle East. The next most important component of genetic variation is apparently associated with a north-south gradient possibly due to adaptation to cold climates but also to the differentiation of the Uralic and the Indo-European language-speaking people; however, the relevant correlations are not significantly different from zero after elimination of the spatial autocorrelation. The third component is highly correlated with the infiltration of the Yamna ("Kurgan") people, nomadic pastoralists who domesticated the horse and who have been claimed to have spread Indo-European languages to Europe; this association, which is statistically significant even when taking spatial autocorrelations into account, does not completely exclude the hypothesis of Indo-European as the language of Neolithic farmers. It is possible that both expansions were responsible for the spread of different subfamilies of Indo-European languages, but our genetic data cannot resolve their relative importance.

High resolution of human evolutionary trees with polymorphic microsatellites.

Genetic variation at hypervariable loci is being used extensively for linkage analysis and individual identification, and may be useful for inter-population studies. Here we show that polymorphic microsatellites (primarily CA repeats) allow trees of human individuals to be constructed that reflect their geographic origin with remarkable accuracy. This is achieved by the analysis of a large number of loci for each individual, in spite of the small variations in allele frequencies existing between populations. Reliable evolutionary relationships could also be established in comparisons among human populations but not among great ape species, probably because of constraints on allele length variation. Among human populations, diversity of microsatellites is highest in Africa, which is in contrast to other nuclear markers and supports the hypothesis of an African origin for humans.

Strengthening hospital nursing, Part III. Differences among professional groups in the hospital planning process.

Interdisciplinary hospital planning processes are examined. Nurses, physicians, hospital administrators, and support and ancillary personnel from 75 hospitals participating in the national Strengthening Hospital Nursing Program indicate their perceptions of the project in relation to the centrality of the program in their hospitals, planning team development, and political issues. Differences and similarities among the professional groups are discussed. Additional articles on the Strengthening Hospital Nursing Program have appeared in the May and June 1992 issues of JONA. Part 1 explored the planning process in single and consortium hospital sites, and Part 2 examined the characteristics of effective planning processes.

Coevolution of genes and languages revisited.

In an earlier paper it was shown that linguistic families of languages spoken by a set of 38 populations associate rather strongly with an evolutionary tree of the same populations derived from genetic data. While the correlation was clearly high, there was no evaluation of statistical significance; no such test was available at the time. This gap has now been filled by adapting to this aim a procedure based on the consistency index, and the level of significance is found to be much stronger than 10(-3). Possible reasons for coevolution of strictly genetic characters and the strictly cultural linguistic system are discussed briefly. Results of this global analysis are compared with those obtained in independent local analysis.

Strengthening hospital nursing, Part 2. Characteristics of effective planning processes.

Characteristics of the planning process for 213 hospitals participating in Phase 1 of the Strengthening Hospital Nursing Program (SHNP) are described. Differences in planning between the Phase 2 implementation sites and those sites not selected for continued funding are explored. Factors associated with positive planning outcomes among participating hospitals are delineated. The use of the SHNP planning process as a model for other hospitals is suggested. This article is Part 2 of a 3-part series on the planning process within the national Strengthening Hospital Nursing Program. Part 1, contrasting single and networked hospitals, appeared in the May issue of JONA. Part 3, which examines interdisciplinary differences, will appear in the July/August issue.

Strengthening hospital nursing. Part 1, The planning process.

Planning is identified as a key activity of hospital management. Planning processes are examined for 75 hospitals in the national Strengthening Hospital Nursing Program (SHNP). The nature of the planning process is presented with a focus on professional participation in planning, differences between single and networked hospitals, and the development of planning teams. The importance of certain elements for planning teams is considered. Part 2 (June 1992 issue) will examine the planning characteristics between Phase 2 selected and nonselected hospitals. Part 3 will explore the differences among professional disciplines in planning.