THE EVOLUTIONARY RELATIONSHIPS OF THE ENZYMES INVOLVED IN BLOOD COAGULATION AND HEMOSTASIS *

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/73621/1/j.1749-6632.1981.tb29759.x.pd

Exponential families of mixed Poisson distributions

If I=(I1,…,Id) is a random variable on [0,∞)d with distribution μ(dλ1,…,dλd), the mixed Poisson distribution MP(μ) on View the MathML source is the distribution of (N1(I1),…,Nd(Id)) where N1,…,Nd are ordinary independent Poisson processes which are also independent of I. The paper proves that if F is a natural exponential family on [0,∞)d then MP(F) is also a natural exponential family if and only if a generating probability of F is the distribution of v0+v1Y1+cdots, three dots, centered+vqYq for some qless-than-or-equals, slantd, for some vectors v0,…,vq of [0,∞)d with disjoint supports and for independent standard real gamma random variables Y1,…,Yq

The evolving (re)categorisations of refugees throughout the ‘Refugee/Migrant crisis’

The UK media’s reporting of events in 2015 contained constantly evolving categorisations of people attempting to reach Europe and the UK, each with different implications for their treatment. A discursive analysis of UK media outputs charts the development of the terminology used to present the ‘crisis’ and those people involved. First ‘Mediterranean migrant crisis’ was used to present those involved as ‘migrants’ to be prevented from reaching Europe. Next it became a ‘Calais Migrant crisis’ in which ‘migrants’ were constructed as a threat to UK security, and then the ‘European Migrant crisis’ an ongoing threat to Europe. Photographs of a drowned child led to a shift to a ‘refugee crisis’ in which ‘refugees’ were presented in a humane and sympathetic way. When terrorist attacks were linked with the ‘crisis’ ‘refugees’ reverted to ‘migrants’. Findings are discussed regarding the impact of categorisation on debates about the inclusion and exclusion of refugees

Representing finite convex geometries by relatively convex sets

A closure system with the anti-exchange axiom is called a convex geometry. One geometry is called a sub-geometry of the other if its closed sets form a sublattice in the lattice of closed sets of the other. We prove that convex geometries of relatively convex sets in $n$-dimensional vector space and their finite sub-geometries satisfy the $n$-Carousel Rule, which is the strengthening of the $n$-Carath$\acute{e}$odory property. We also find another property, that is similar to the simplex partition property and does not follow from $2$-Carusel Rule, which holds in sub-geometries of $2$-dimensional geometries of relatively convex sets.Comment: 12 page

Agricultural Turns, Geographical Turns: Retrospect and Prospect.

It is accepted that British rural geography has actively engaged with the ‘cultural turn’, leading to a resurgence of research within the sub-discipline. However, a reading of recent reviews suggests that the cultural turn has largely, if not completely, bypassed those geographers interested in the agricultural sector. Farming centred engagements with notions of culture have been relatively limited compared with those concerned with the non-agricultural aspects of rural space. Indeed, agricultural geography represents something of an awkward case in the context of the disciplinary turn to culture, a situation that demands further exposition. In seeking explanation, it becomes evident that research on the farm sector is more culturally informed than initially appears. This paper argues that there have been both interesting and important engagements between agricultural geography and cultural perspectives over the past decade. The paper elaborates four specific areas of research which provide evidence for concern about the ‘culture’ within agriculture. The future contribution that culturally informed perspectives in geographical research can bring to agricultural issues is outlined by way of conclusion

OCPAT: an online codon-preserved alignment tool for evolutionary genomic analysis of protein coding sequences

<p>Abstract</p> <p>Background</p> <p>Rapidly accumulating genome sequence data from multiple species offer powerful opportunities for the detection of DNA sequence evolution. Phylogenetic tree construction and codon-based tests for natural selection are the prevailing tools used to detect functionally important evolutionary change in protein coding sequences. These analyses often require multiple DNA sequence alignments that maintain the correct reading frame for each collection of putative orthologous sequences. Since this feature is not available in most alignment tools, codon reading frames often must be checked manually before evolutionary analyses can commence.</p> <p>Results</p> <p>Here we report an online codon-preserved alignment tool (OCPAT) that generates multiple sequence alignments automatically from the coding sequences of any list of human gene IDs and their putative orthologs from genomes of other vertebrate tetrapods. OCPAT is programmed to extract putative orthologous genes from genomes and to align the orthologs with the reading frame maintained in all species. OCPAT also optimizes the alignment by trimming the most variable alignment regions at the 5' and 3' ends of each gene. The resulting output of alignments is returned in several formats, which facilitates further molecular evolutionary analyses by appropriate available software. Alignments are generally robust and reliable, retaining the correct reading frame. The tool can serve as the first step for comparative genomic analyses of protein-coding gene sequences including phylogenetic tree reconstruction and detection of natural selection. We aligned 20,658 human RefSeq mRNAs using OCPAT. Most alignments are missing sequence(s) from at least one species; however, functional annotation clustering of the ~1700 transcripts that were alignable to all species shows that genes involved in multi-subunit protein complexes are highly conserved.</p> <p>Conclusion</p> <p>The OCPAT program facilitates large-scale evolutionary and phylogenetic analyses of entire biological processes, pathways, and diseases.</p

The Milky Way's Fermi Bubbles: Echoes of the Last Quasar Outburst?

{\it Fermi}-LAT has recently detected two gamma ray bubbles disposed symmetrically with respect to the Galactic plane. The bubbles have been suggested to be in a quasi-steady state, inflated by ongoing star formation over the age of the Galaxy. Here we propose an alternative picture where the bubbles are the remnants of a large-scale wide-angle outflow from \sgra, the SMBH of our Galaxy. Such an outflow would be a natural consequence of a short but bright accretion event on to \sgra\ if it happened concurrently with the well known star formation event in the inner 0.5 pc of the Milky Way $\sim 6$ Myr ago. We find that the hypothesised near-spherical outflow is focussed into a pair of symmetrical lobes by the greater gas pressure along the Galactic plane. The outflow shocks against the interstellar gas in the Galaxy bulge. Gamma--ray emission could be powered by cosmic rays created by either \sgra\ directly or accelerated in the shocks with the external medium. The Galaxy disc remains unaffected, agreeing with recent observational evidence that supermassive black holes do not correlate with galaxy disc properties. We estimate that an accreted mass \sim 2 \times 10^3\msun is needed for the accretion event to power the observed {\it Fermi}--LAT lobes. Within a factor of a few this agrees with the mass of the young stars born during the star formation event. This estimate suggests that roughly 50% of the gas was turned into stars, while the rest accreted onto \sgra. One interpretation of this is a reduced star formation efficiency inside the \sgra\ accretion disc due to stellar feedback, and the other a peculiar mass deposition geometry that resulted in a significant amount of gas falling directly inside the inner $\sim 0.03$ pc of the Galaxy.Comment: 6 pages, 0 figures; accepted for publication in MNRA

Molecular evolution of the cytochrome c oxidase subunit 5A gene in primates

Abstract Background Many electron transport chain (ETC) genes show accelerated rates of nonsynonymous nucleotide substitutions in anthropoid primate lineages, yet in non-anthropoid lineages the ETC proteins are typically highly conserved. Here, we test the hypothesis that COX5A, the ETC gene that encodes cytochrome c oxidase subunit 5A, shows a pattern of anthropoid-specific adaptive evolution, and investigate the distribution of this protein in catarrhine brains. Results In a dataset comprising 29 vertebrate taxa, including representatives from all major groups of primates, there is nearly 100% conservation of the COX5A amino acid sequence among extant, non-anthropoid placental mammals. The most recent common ancestor of these species lived about 100 million years (MY) ago. In contrast, anthropoid primates show markedly elevated rates of nonsynonymous evolution. In particular, branch site tests identify five positively selected codons in anthropoids, and ancestral reconstructions infer that substitutions in these codons occurred predominantly on stem lineages (anthropoid, ape and New World monkey) and on the human terminal branch. Examination of catarrhine brain samples by immunohistochemistry characterizes for the first time COX5A protein distribution in the primate neocortex, and suggests that the protein is most abundant in the mitochondria of large-size projection neurons. Real time quantitative PCR supports previous microarray results showing COX5A is expressed in cerebral cortical tissue at a higher level in human than in chimpanzee or gorilla. Conclusion Taken together, these results suggest that both protein structural and gene regulatory changes contributed to COX5A evolution during humankind\u27s ancestry. Furthermore, these findings are consistent with the hypothesis that adaptations in ETC genes contributed to the emergence of the energetically expensive anthropoid neocortex