One-dimensional fluids with second nearest-neighbor interactions

As is well known, one-dimensional systems with interactions restricted to first nearest neighbors admit a full analytically exact statistical-mechanical solution. This is essentially due to the fact that the knowledge of the first nearest-neighbor probability distribution function, $p_1(r)$, is enough to determine the structural and thermodynamic properties of the system. On the other hand, if the interaction between second nearest-neighbor particles is turned on, the analytically exact solution is lost. Not only the knowledge of $p_1(r)$ is not sufficient anymore, but even its determination becomes a complex many-body problem. In this work we systematically explore different approximate solutions for one-dimensional second nearest-neighbor fluid models. We apply those approximations to the square-well and the attractive two-step pair potentials and compare them with Monte Carlo simulations, finding an excellent agreement.Comment: 26 pages, 12 figures; v2: more references adde

Hybrid assembly with long and short reads improves discovery of gene family expansions

BACKGROUND: Long-read and short-read sequencing technologies offer competing advantages for eukaryotic genome sequencing projects. Combinations of both may be appropriate for surveys of within-species genomic variation. METHODS: We developed a hybrid assembly pipeline called "Alpaca" that can operate on 20X long-read coverage plus about 50X short-insert and 50X long-insert short-read coverage. To preclude collapse of tandem repeats, Alpaca relies on base-call-corrected long reads for contig formation. RESULTS: Compared to two other assembly protocols, Alpaca demonstrated the most reference agreement and repeat capture on the rice genome. On three accessions of the model legume Medicago truncatula, Alpaca generated the most agreement to a conspecific reference and predicted tandemly repeated genes absent from the other assemblies. CONCLUSION: Our results suggest Alpaca is a useful tool for investigating structural and copy number variation within de novo assemblies of sampled populations

Testing Kaldor’s Growth Laws Across the Countries of Africa.

One of the strong factors reflecting Africa's economic backwardness is the low level of industrial development. Not only does the industrialization process appear to have bypassed the continent, there is evidence of de-industrialization in the case of several countries. This paper seeks to address a set of interrelated questions: To what extent is the growth performance of African economies related to these structural characteristics? More precisely, is there any discernible evidence that GDP growth and overall labour productivity growth of African countries is positively related to how fast their industrial sector is growing? We test out Kaldor's three growth laws: first, that the growth of GDP is positively related to the growth of manufacturing output not simply in a definitional sense (because manufacturing output is a part of GDP) but in a fundamental causal sense related to the production characteristics of manufacturing activity; secondly, that the growth of labour productivity in manufacturing is positively related to manufacturing output growth because of static and dynamic increasing returns to scale (Verdoorn's Law); and thirdly, that there will be a negative relation between labour productivity growth in the economy as a whole and the rate of growth of employment in the non-manufacturing sector because most activity outside the manufacturing sector is subject to diminishing returns, particularly in land-based activities such as agriculture and many service activities. The authors' conclusions are that there is some empirical support for Kaldor's growth laws in respect of the countries of Africa. The growth of GDP seems much more closely associated with the growth of the manufacturing/industrial sector than the agricultural or service sectors. Structural change in favour of industrial activities would almost certainly help to accelerate the growth of GDP and living standards in Africa

RETURNS TO SCALE AND REGIONAL GROWTH: THE STATIC-DYNAMIC VERDOORN LAW PARADOX REVISITED

It has long been an article of faith amongst regional economists that increasing returns to scale are necessary to explain the punctiform location of economic activity and population. However, there is no consensus in the empirical literature over whether returns to scale are constant or increasing. A notable example of this lack of agreement is provided by the static-dynamic Verdoorn law paradox. While the dynamic Verdoorn law (specified using growth rates) yields estimates of substantial increasing returns to scale, the static Verdoorn law (specified using log-levels) indicates only the presence of constant returns to scale. In this paper, we explain the static-dynamic Verdoorn law paradox by showing that estimates of returns to scale obtained using the static law are subject to a spatial aggregation bias, which biases the estimates towards constant returns to scale. We illustrate our arguments by means of simulation exercises. The results obtained hold general lessons for applied economic analysis using spatial data. Copyright Blackwell Publishing, Inc. 2007

Evolution and microsynteny of the apyrase gene family in three legume genomes

Apyrases have been suggested to play important roles in plant nutrition, photomorphogenesis, and nodulation. To help trace the evolution of these genes in the legumes-and possibly, the acquisition of new functions for nodulation-apyrase-containing BACs were sequenced from three legume genomes. Genomic sequences from Medicago truncatula, Glycine max and Lotus japonicus were compared to one another and to corresponding regions in Arabidopsis thaliana. A phylogenetic analysis of apyrase homologs from these regions and sequences from other legume species, as well as other plant families, identified a potentially legume-specific clade that contains a well-characterized soybean ( G. soja) apyrase, Gs52, as well as homologs from Dolichos, Lotus , Medicago and Pisum. Sister clades contain homologs from members of Brassicaceae, Solanaceae, Poaceae and Fabaceae. Comparisons of rates of change at synonymous and nonsynonymous sites in the Gs52 and sister clades show rapid evolution in the potentially legume-specific Gs52 clade. The genomic organization of the apyrase-containing BACs shows evidence of gene duplication, genomic rearrangement, and gene conversion among Gs52 homologs. Taken together, these results suggest a scenario of local apyrase gene duplication in an ancestor of the legumes, followed by functional diversification and increased rates of change in the new genes, and further duplications in the Galegae (which include the genera Medicago and Pisum). The study also provides a detailed comparison of genomic regions between two model genomes which are now being sequenced ( M. truncatula and L. japonicus), and a genome from an economically important legume species (G. max)