edgeRun: an R package for sensitive, functionally relevant differential expression discovery using an unconditional exact test.

UNLABELLED: Next-generation sequencing platforms for measuring digital expression such as RNA-Seq are displacing traditional microarray-based methods in biological experiments. The detection of differentially expressed genes between groups of biological conditions has led to the development of numerous bioinformatics tools, but so far, few exploit the expanded dynamic range afforded by the new technologies. We present edgeRun, an R package that implements an unconditional exact test that is a more powerful version of the exact test in edgeR. This increase in power is especially pronounced for experiments with as few as two replicates per condition, for genes with low total expression and with large biological coefficient of variation. In comparison with a panel of other tools, edgeRun consistently captures functionally similar differentially expressed genes. AVAILABILITY AND IMPLEMENTATION: The package is freely available under the MIT license from CRAN (http://cran.r-project.org/web/packages/edgeRun). CONTACT: [email protected] SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online

Population genetics of trypanosoma brucei rhodesiense: clonality and diversity within and between foci

African trypanosomes are unusual among pathogenic protozoa in that they can undergo their complete morphological life cycle in the tsetse fly vector with mating as a non-obligatory part of this development. Trypanosoma brucei rhodesiense, which infects humans and livestock in East and Southern Africa, has classically been described as a host-range variant of the non-human infective Trypanosoma brucei that occurs as stable clonal lineages. We have examined T. b. rhodesiense populations from East (Uganda) and Southern (Malawi) Africa using a panel of microsatellite markers, incorporating both spatial and temporal analyses. Our data demonstrate that Ugandan T. b. rhodesiense existed as clonal populations, with a small number of highly related genotypes and substantial linkage disequilibrium between pairs of loci. However, these populations were not stable as the dominant genotypes changed and the genetic diversity also reduced over time. Thus these populations do not conform to one of the criteria for strict clonality, namely stability of predominant genotypes over time, and our results show that, in a period in the mid 1990s, the previously predominant genotypes were not detected but were replaced by a novel clonal population with limited genetic relationship to the original population present between 1970 and 1990. In contrast, the Malawi T. b. rhodesiense population demonstrated significantly greater diversity and evidence for frequent genetic exchange. Therefore, the population genetics of T. b. rhodesiense is more complex than previously described. This has important implications for the spread of the single copy T. b. rhodesiense gene that allows human infectivity, and therefore the epidemiology of the human disease, as well as suggesting that these parasites represent an important organism to study the influence of optional recombination upon population genetic dynamics

Concurrence in Disordered Systems

Quantum systems exist at finite temperatures and are likely to be disordered to some level. Since applications of quantum information often rely on entanglement, we require methods which allow entanglement measures to be calculated in the presence of disorder at non-zero temperatures. We demonstrate how the disorder averaged concurrence can be calculated using thermal many-body perturbation theory. Our technique can also be applied to other entanglement measures. To illustrate, we find the disorder averaged concurrence of an XX spin chain. We find that concurrence can be increased by disorder in some parameter regimes.Comment: 14 pages, 5 figure

Relationship between photonic band structure and emission characteristics of a polymer distributed feedback laser

G. A. Turnbull, P. Andrew, M. J. Jory, William L. Barnes, and I. D. W. Samuel, Physical Review B, Vol. 64, article 125122 (2001). "Copyright © 2001 by the American Physical Society."We present an experimental study of the emission characteristics and photonic band structure of a distributed feedback polymer laser, based on the material poly[2-methoxy-5-(2′-ethylhexyloxy)-1,4-phenylene vinylene]. We use measurements of the photonic band dispersion to explain how the substrate microstructure modifies both spontaneous and stimulated emission. The lasing structure exhibits a one-dimensional photonic band gap around 610 nm, with lasing occurring at one of the two associated band edges. The band edge (frequency) selection mechanism is found to be a difference in the level of output coupling of the modes associated with the two band edges. This is a feature of the second-order distributed feedback mechanism we have employed and is clearly evident in the measured photonic band structur

Differences between <i>Trypanosoma brucei gambiense</i> groups 1 and 2 in their resistance to killing by Trypanolytic factor 1

&lt;p&gt;&lt;b&gt;Background:&lt;/b&gt; The three sub-species of &lt;i&gt;Trypanosoma brucei&lt;/i&gt; are important pathogens of sub-Saharan Africa. &lt;i&gt;T. b. brucei&lt;/i&gt; is unable to infect humans due to sensitivity to trypanosome lytic factors (TLF) 1 and 2 found in human serum. &lt;i&gt;T. b. rhodesiense&lt;/i&gt; and &lt;i&gt;T. b. gambiense&lt;/i&gt; are able to resist lysis by TLF. There are two distinct sub-groups of &lt;i&gt;T. b. gambiense&lt;/i&gt; that differ genetically and by human serum resistance phenotypes. Group 1 &lt;i&gt;T. b. gambiense&lt;/i&gt; have an invariant phenotype whereas group 2 show variable resistance. Previous data indicated that group 1 &lt;i&gt;T. b. gambiense&lt;/i&gt; are resistant to TLF-1 due in-part to reduced uptake of TLF-1 mediated by reduced expression of the TLF-1 receptor (the haptoglobin-hemoglobin receptor (&lt;i&gt;HpHbR&lt;/i&gt;)) gene. Here we investigate if this is also true in group 2 parasites.&lt;/p&gt; &lt;p&gt;&lt;b&gt;Methodology:&lt;/b&gt; Isogenic resistant and sensitive group 2 &lt;i&gt;T. b. gambiense&lt;/i&gt; were derived and compared to other T. brucei parasites. Both resistant and sensitive lines express the &lt;i&gt;HpHbR&lt;/i&gt; gene at similar levels and internalized fluorescently labeled TLF-1 similar fashion to &lt;i&gt;T. b. brucei&lt;/i&gt;. Both resistant and sensitive group 2, as well as group 1 &lt;i&gt;T. b. gambiense&lt;/i&gt;, internalize recombinant APOL1, but only sensitive group 2 parasites are lysed.&lt;/p&gt; &lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; Our data indicate that, despite group 1 &lt;i&gt;T. b. gambiense&lt;/i&gt; avoiding TLF-1, it is resistant to the main lytic component, APOL1. Similarly group 2 &lt;i&gt;T. b. gambiense&lt;/i&gt; is innately resistant to APOL1, which could be based on the same mechanism. However, group 2 &lt;i&gt;T. b. gambiense&lt;/i&gt; variably displays this phenotype and expression does not appear to correlate with a change in expression site or expression of &lt;i&gt;HpHbR&lt;/i&gt;. Thus there are differences in the mechanism of human serum resistance between &lt;i&gt;T. b. gambiense&lt;/i&gt; groups 1 and 2.&lt;/p&gt

New Ireland Province: Text summaries, maps, code lists and village identification

The major purpose of the Papua New Guinea Agricultural Systems Project is to produce information on small holder (subsistence) agriculture at provincial and national levels (Allen et al 1995). Information was collected by field observation, interviews with villagers and reference to published and unpublished documents. Methods are described by Bourke et al. (1993). This Working Paper contains a written summary of the information on the Agricultural Systems in this Province, maps of the location of agriculture systems, a complete listing of all information in the database in coded form, and lists of villages with National Population Census codes, indexed by agricultural systems. This information is available as a map-linked database (GIS) suitable for use on a personal computer in ESRI and MapInfo formats. An Agricultural System is identified when a set of similar agricultural crops and practices occur within a defined area. Six criteria are used to distinguish one system from another: 1. Fallow type (the vegetation which is cleared from a garden site before cultivation). 2. Fallow period (the length of time a garden site is left unused between cultivations). 3. Cultivation intensity (the number of consecutive crops planted before fallow). 4. The staple, or most important, crops. 5. Garden and crop segregation (the extent to which crops are planted in separate gardens; in separate areas within a garden; or are planted sequentially). 6. Soil fertility maintenance techniques (other than natural regrowth fallows). Where one or more of these factors differs significantly and the differences can be mapped, then a separate system is distinguished. Where variation occurs, but is not able to be mapped at 1:500 000 scale because the areas in which the variation occurs are too small or are widely dispersed within the larger system, a subsystem is identified. Subsystems within an Agricultural System are allocated a separate record in the database, identified by the Agricultural System number and a subsystem number. Sago is a widespread staple food in lowland Papua New Guinea. Sago is produced from palms which are not grown in gardens. Most of the criteria above cannot be applied. In this case, systems are differentiated on the basis of the staple crops only. The Papua New Guinea Resource Information System (PNGRIS) is a GIS which contains information on the natural resources of PNG (Bellamy 1986). PNGRIS contains no information on agricultural practices, other than an assessment of land use intensity based on air photograph interpretation by Saunders (1993. The Agricultural Systems Project is designed to provide detailed information on agricultural practices and cropping patterns as part of an upgraded PNGRIS geographical information system. For this reason the Agricultural Systems database contains almost no information on the environmental settings of the systems, except for altitude and slope. The layout of the text descriptions, the database code files and the village lists are similar to PNGRIS formats (Cuddy 1987). The mapping of Agricultural Systems has been carried out on the same map base and scale as PNGRIS (Tactical Pilotage Charts, 1:500 000). Agricultural Systems were mapped within the areas of agricultural land use established by Saunders (1993) from aerial photography. Except where specifically noted, Agricultural Systems boundaries have been mapped without reference to PNGRIS Resource Mapping Unit (RMU) boundaries. Agricultural Systems are defined at the level of the Province (following PNGRIS) but their wider distribution is recognised in the database by cross-referencing systems which cross provincial borders. A preliminary view of the relationships between PNGRIS RMUs and the Agricultural Systems in this Province can be obtained from the listing of villages by Agricultural System, where RMU numbers are appended. Allen, B. J., R. M. Bourke and R. L. Hide 1995. The sustainability of Papua New Guinea agricultural systems: the conceptual background. Global Environmental Change 5(4): 297-312. Bourke, R. M., R. L. Hide, B. J. Allen, R. Grau, G. S. Humphreys and H. C. Brookfield 1993. Mapping agricultural systems in Papua New Guinea. Population Family Health and Development. T. Taufa and C. Bass. University of Papua New Guinea Press, Port Moresby: 205-224. Bellamy, J. A. and J. R. McAlpine 1995. Papua New Guinea Inventory of Natural Resources, Population Distribution and Land Use Handbook. Commonwealth Scientific and Industrial Research Organisation for the Australian Agency for International Development. PNGRIS Publication No. 6, Canberra. Cuddy, S. M. 1987. Papua New Guinea Inventory of Natural Resources, Population Distribution and Land Use: Code Files Part 1 Natural Resources. Division of Water and Land Resources, Commonwealth Scientific and Industrial Research Organisation and Land Utilization Section, Department of Primary Industry, Papua New Guinea, Canberra

An extended massless phase and the Haldane phase in a spin-1 isotropic antiferromagnetic chain

We study the phase transition of isotropic spin-1 models in the vicinity of the Uimin-Lai-Sutherland model by using the SU(3)_1 WZW model with certain marginal perturbations. The unstable RG trajectory by a marginally relevant perturbation generates a mass gap for the Haldane phase, and thus the universality class of the transition from the massless phase to the Haldane phase at ULS point becomes the BKT type. Our results support recent numerical studies by F\'ath and S\'olyom. In the massless phase, we calculate logarithmic finite-size corrections of the energy for the SU(\nu)-symmetric and asymmetric models.Comment: 19 pages, RevTe

Photonic mode dispersion of a two-dimensional distributed feedback polymer laser

G. A. Turnbull, P. Andrew, William L. Barnes, and I. D. W. Samuel, Physical Review B, Vol. 67, article 165107 (2003). "Copyright © 2003 by the American Physical Society."We present an analysis of the photonic mode dispersion of a two-dimensional (2D) distributed feedback polymer laser based on the conjugated polymer poly[2-methoxy-5-(2′-ethylhexyloxy)-1,4-phenylene vinylene]. We use a combination of a simple model, together with experimental measurements of the photonic mode dispersion in transmission and emission, to explain the operating characteristics of the laser. The laser was found to oscillate at 636 nm on one edge of a photonic stop band in the photonic dispersion. A 2D coupling of modes traveling perpendicular to the orthogonal gratings was found to lead to a low divergence laser emission normal to the waveguide. At pump energies well above the oscillation threshold for this mode, a divergent, cross-shaped far-field emission was observed, resulting from a distributed feedback occurring over a wide range of wave vectors in one band of the photonic dispersion