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

The Malkus–Robbins dynamo with a linear series motor

Hide [1997] has introduced a number of different nonlinear models to describe the behavior of n-coupled self-exciting Faraday disk homopolar dynamos. The hierarchy of dynamos based upon the Hide et al. [1996] study has already received much attention in the literature (see [Moroz, 2001] for a review). In this paper we focus upon the remaining dynamo, namely Case 3 of [Hide, 1997] for the particular limit in which the Malkus–Robbins dynamo [Malkus, 1972; Robbins, 1997] obtains, but now modified by the presence of a linear series motor. We compare and contrast the linear and the nonlinear behaviors of the two types of dynamo

R-modes in the ocean of a magnetic neutron star

We study the dynamics of r-modes in the ocean of a magnetic neutron star. We modeled the star's ocean with a spherical rotating thin shell and assumed that the magnetic field symmetry axis is not aligned to the shell's spin axis. In the magnetohydrodynamic approximation, we calculate the frequency of $\ell=m$ r-modes in the shell of an incompressible fluid. Different r-modes with $\ell$ and $\ell\pm2$ are coupled by the {\it inclined} magnetic field. Kinematical secular effects for the motion of a fluid element in the shell undergoing $\ell=m=2$ r-mode are studied. The magnetic corrected drift velocity of a given fluid element undergoing the $\ell=m$ r-mode oscillations is obtained. The magnetic field increases the magnitude of the fluid drift produced by the r-mode drift velocity, the high-$\ell$ modes in the ocean fluid will damp faster than the low-$\ell$ ones.Comment: 24 pages, 5 figures, to appear in ApJ, v574 n2 August 1, 2002 issu

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

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

Western 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

Divergent LIN28-mRNA associations result in translational suppression upon the initiation of differentiation

LIN28 function is fundamental to the activity and behavior of human embryonic stem cells (hESCs) and induced pluripotent stem cells. Its main roles in these cell types are the regulation of translational efficiency and let-7 miRNA maturation. However, LIN28-associated mRNA cargo shifting and resultant regulation of translational efficiency upon the initiation of differentiation remain unknown. An RNA-immunoprecipitation and microarray analysis protocol, eRIP, that has high specificity and sensitivity was developed to test endogenous LIN28-associated mRNA cargo shifting. A combined eRIP and polysome analysis of early stage differentiation of hESCs with two distinct differentiation cues revealed close similarities between the dynamics of LIN28 association and translational modulation of genes involved in the Wnt signaling, cell cycle, RNA metabolism and proteasomal pathways. Our data demonstrate that change in translational efficiency is a major contributor to early stages of differentiation of hESCs, in which LIN28 plays a central role. This implies that eRIP analysis of LIN28-associated RNA cargoes may be used for rapid functional quality control of pluripotent stem cells under manufacture for therapeutic applications

Mountain torques and atmospheric oscillations

Theoretical work and general circulation model (GCM) experiments suggest that the midlatitude jet stream's interaction with large‐scale topography can drive intraseasonal oscillations in large‐scale atmospheric circulation patterns. In support of this theory, we present new observational evidence that mountain‐induced torques play a key role in 15–30‐day oscillations of the Northern Hemisphere circulation's dominant patterns. The affected patterns include the Arctic Oscillation (AO) and the Pacific‐North‐American (PNA) pattern. Positive torques both accelerate and anticipate the midlatitude westerly winds at these periodicities. Moreover, torque anomalies anticipate the onsets of weather regimes over the Pacific, as well as the break‐ups of hemispheric‐scale regimes

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

Region-Based Analysis of Rare Genomic Variants in Whole-Genome Sequencing Datasets Reveal Two Novel Alzheimer’s Disease-Associated Genes: \u3cem\u3eDTNB\u3c/em\u3e and \u3cem\u3eDLG2\u3c/em\u3e

Alzheimer’s disease (AD) is a genetically complex disease for which nearly 40 loci have now been identified via genome-wide association studies (GWAS). We attempted to identify groups of rare variants (alternate allele frequency \u3c0.01) associated with AD in a region-based, whole-genome sequencing (WGS) association study (rvGWAS) of two independent AD family datasets (NIMH/NIA; 2247 individuals; 605 families). Employing a sliding window approach across the genome, we identified several regions that achieved association p values \u3c10−6, using the burden test or the SKAT statistic. The genomic region around the dystobrevin beta (DTNB) gene was identified with the burden and SKAT test and replicated in case/control samples from the ADSP study reaching genome-wide significance after meta-analysis (pmeta= 4.74 × 10−8 ). SKAT analysis also revealed region-based association around the Discs large homolog 2 (DLG2) gene and replicated in case/control samples from the ADSP study (pmeta = 1 × 10−6 ). In conclusion, in a region-based rvGWAS of AD we identified two novel AD genes, DLG2 and DTNB, based on association with rare variants