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Effect of intrarow plant spacing on the effectiveness of family selection in sugarcane: Selection indices
De Sousa-Vieira,Orlando; Milligan,Scott B;
Interciencia , 2009,
Abstract: cross prediction trials or progeny tests for family selection are commonly employed at the beginning of each breeding cycle in clonally propagated crops such as sugarcane (saccharum spp. hybrid). when selecting sugarcane families, the factors affecting variability between and within those families should be considered. this research examined the influence of family and intra-row plant spacing on the efficiency of the index selection procedure as a method of simultaneous improvement of a population for multiple traits at the first selection stage of the louisiana sugarcane variety development program (lsvdp). therefore, the main objective of this study was to develop a selection index for selecting sugarcane families within the lsvdp. expected genetic advance values for plant weight were greater in the wide-spaced indices than in the narrow-spaced ones. irrespective of plant spacing, selection indices revealed that an increase in efficiency was observed over direct selection for plant weight when all four plant weight contributing traits were included along with plant weight. the efficiency in selection tended to decrease when indices were based on fewer traits. nevertheless, a few of the indices that included two traits had relative efficiencies comparable to the best indices and the majority certainly was as effective as direct selection for plant weight.
Interrelationships of cane yield components and their utility in sugarcane family selection: Path coefficient analysis
De Sousa-Vieira,Orlando; Milligan,Scott B;
Interciencia , 2005,
Abstract: progeny testing is used to identify sugarcane families with superior, stable performance at the first selection stage of the louisiana sugarcane variety development program, usa (lsvdp). research to optimize the current progeny-testing methodology examined the relative importance of family and intra-row plant spacing in terms of effectiveness of the testing procedure. knowledge of the interrelationship among the various traits considered important in selection plays an important role in the success of the lsvdp. path coefficient analysis was used to measure the direct and indirect influence of plant weight components on the estimation of plant weight by partitioning phenotypic and genotypic correlation coefficients into components of direct and indirect effects. phenotypic and genotypic direct effects were all positive, indicating that selection for any of the plant weight components should translate into an increase in plant weight. number of stalks per plant, stalk diameter, and stalk length accounted for almost all of the variation in plant weight as indicated by the coefficient of determination. irrespective of plant spacing, path coefficients revealed that, relative to the correlation coefficients values, stalk diameter and number of stalks per plant had the largest direct positive effect on plant weight at both phenotypic and genotypic levels.
Estimating and Analyzing Demographic Models Using the popbio Package in R
Chris Stubben,Brook Milligan
Journal of Statistical Software , 2007,
Abstract: A complete assessment of population growth and viability from field census data often requires complex data manipulations, statistical routines, mathematical tools, programming environments, and graphical capabilities. We therefore designed an R package called popbio to facilitate both the construction and analysis of projection matrix models. The package consists primarily of the R translation of MATLAB code found in Caswell (2001) and Morris and Doak (2002) for the analysis of projection matrix models. The package also includes methods to estimate vital rates and construct projection matrix models from census data typically collected in plant demography studies. In these studies, vital rates can often be estimated directly from annual censuses of tagged individuals using transition frequency tables. Because the construction of projection matrix models requires careful management of census data, we describe the steps to construct a projection matrix in detail.
Accurate Diagnostics for Bovine tuberculosis Based on High-Throughput Sequencing
Alexander Churbanov, Brook Milligan
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0050147
Abstract: Background Bovine tuberculosis (bTB) is an enduring contagious disease of cattle that has caused substantial losses to the global livestock industry. Despite large-scale eradication efforts, bTB continues to persist. Current bTB tests rely on the measurement of immune responses in vivo (skin tests), and in vitro (bovine interferon-γ release assay). Recent developments are characterized by interrogating the expression of an increasing number of genes that participate in the immune response. Currently used assays have the disadvantages of limited sensitivity and specificity, which may lead to incomplete eradication of bTB. Moreover, bTB that reemerges from wild disease reservoirs requires early and reliable diagnostics to prevent further spread. In this work, we use high-throughput sequencing of the peripheral blood mononuclear cells (PBMCs) transcriptome to identify an extensive panel of genes that participate in the immune response. We also investigate the possibility of developing a reliable bTB classification framework based on RNA-Seq reads. Methodology/Principal Findings Pooled PBMC mRNA samples from unaffected calves as well as from those with disease progression of 1 and 2 months were sequenced using the Illumina Genome Analyzer II. More than 90 million reads were splice-aligned against the reference genome, and deposited to the database for further expression analysis and visualization. Using this database, we identified 2,312 genes that were differentially expressed in response to bTB infection (p<10?8). We achieved a bTB infected status classification accuracy of more than 99% with split-sample validation on newly designed and learned mixtures of expression profiles. Conclusions/Significance We demonstrated that bTB can be accurately diagnosed at the early stages of disease progression based on RNA-Seq high-throughput sequencing. The inclusion of multiple genes in the diagnostic panel, combined with the superior sensitivity and broader dynamic range of RNA-Seq, has the potential to improve the accuracy of bTB diagnostics. The computational pipeline used for the project is available from http://code.google.com/p/bovine-tb-predi?ction.
A Hot Microflare Observed With RHESSI and Hinode
Ryan O. Milligan
Physics , 2010, DOI: 10.1086/589856
Abstract: RHESSI and Hinode observations of a GOES B-class flare are combined to investigate the origin of 15 MK plasma. The absence of any detectable hard X-ray emission coupled with weak blueshifted emission lines (indicating upward velocities averaging only 14 km/s) suggests that this was a result of direct heating in the corona, as opposed to nonthermal electron precipitation causing chromospheric evaporation. These findings are in agreement with a recent hydrodynamical simulation of microflare plasmas which found that higher temperatures can be attained when less energy is used to accelerate electrons out of the thermal distribution. In addition, unusual redshifts in the 2 MK Fe XV line (indicating downward velocities of 14 km/s) were observed cospatial with one of the flare ribbons during the event. Downflows of such high temperature plasma are not predicted by any common flare model.
Extreme Ultra-Violet Spectroscopy of the Lower Solar Atmosphere During Solar Flares
Ryan O. Milligan
Physics , 2015, DOI: 10.1007/s11207-015-0748-2
Abstract: The extreme ultraviolet portion of the solar spectrum contains a wealth of diagnostic tools for probing the lower solar atmosphere in response to an injection of energy, particularly during the impulsive phase of solar flares. These include temperature and density sensitive line ratios, Doppler shifted emission lines and nonthermal broadening, abundance measurements, differential emission measure profiles, and continuum temperatures and energetics, among others. In this paper I shall review some of the advances made in recent years using these techniques, focusing primarily on studies that have utilized data from Hinode/EIS and SDO/EVE, while also providing some historical background and a summary of future spectroscopic instrumentation.
Spatially-Resolved Nonthermal Line Broadening During The Impulsive Phase of a Solar Flare
Ryan O. Milligan
Physics , 2012, DOI: 10.1088/0004-637X/740/2/70
Abstract: This paper presents a detailed study of excess line broadening in EUV emission lines during the impulsive phase of a C-class solar flare. In this work, which utilizes data from the EUV Imaging Spectrometer (EIS) onboard Hinode, the broadened line profiles were observed to be co-spatial with the two HXR footpoints as observed by RHESSI. By plotting the derived nonthermal velocity for each pixel within the Fe XV and Fe XVI rasters against its corresponding Doppler velocity a strong correlation (|r| > 0.59) was found between the two parameters for one of the footpoints. This suggested that the excess broadening at these temperatures is due to a superposition of flows (turbulence), presumably as a result of chromospheric evaporation due to nonthermal electrons. Also presented are diagnostics of electron densities using five pairs of density-sensitive line ratios. Density maps derived using the Mg XII and Si X line pairs showed no appreciable increase in electron density at the footpoints, while the Fe XII, Fe XIII, and Fe XIV line pairs revealed densities approaching 10^(11.5) cm^(-3). Using this information, the nonthermal velocities derived from the widths of the two Fe XIV lines were plotted against their corresponding density values derived from their ratio. This showed that pixels with large nonthermal velocities were associated with pixels of moderately higher densities. This suggests that nonthermal broadening at these temperatures may have been due to enhanced densities at the footpoints, although estimates of the amount of opacity broadening and pressure broadening appeared to be negligible.
Using fractional differentiation in astronomy
Amelia Carolina Sparavigna,Paul Milligan
Physics , 2009,
Abstract: In a recent paper, published at arXiv:0910.2381, we started a discussion on the new possibilities arising from the use of fractional differential calculus in image processing. We have seen that the fractional calculation is able to enhance the quality of images, with interesting possibilities in edge detection and image restoration. Here, we want to discuss more deeply its role as a tool for the processing of astronomical images. In particular, the fractional differentiation can help produce a 'content-matter' based image from a pretty astronomical image that can be used for more research and scientific purposes, for instance to reveal faint objects galactic matter, nebulosity, more stars and planetary surface detail.
Identification and Characterization of a Mef2 Transcriptional Activator in Schistosome Parasites
John N. Milligan,Emmitt R. Jolly
PLOS Neglected Tropical Diseases , 2012, DOI: 10.1371/journal.pntd.0001443
Abstract: Myocyte enhancer factor 2 protein (Mef2) is an evolutionarily conserved activator of transcription that is critical to induce and control complex processes in myogenesis and neurogenesis in vertebrates and insects, and osteogenesis in vertebrates. In Drosophila, Mef2 null mutants are unable to produce differentiated muscle cells, and in vertebrates, Mef2 mutants are embryonic lethal. Schistosome worms are responsible for over 200 million cases of schistosomiasis globally, but little is known about early development of schistosome parasites after infecting a vertebrate host. Understanding basic schistosome development could be crucial to delineating potential drug targets. Here, we identify and characterize Mef2 from the schistosome worm Schistosoma mansoni (SmMef2). We initially identified SmMef2 as a homolog to the yeast Mef2 homolog, Resistance to Lethality of MKK1P386 overexpression (Rlm1), and we show that SmMef2 is homologous to conserved Mef2 family proteins. Using a genetics approach, we demonstrate that SmMef2 is a transactivator that can induce transcription of four separate heterologous reporter genes by yeast one-hybrid analysis. We also show that Mef2 is expressed during several stages of schistosome development by quantitative PCR and that it can bind to conserved Mef2 DNA consensus binding sequences.
Collective Learning in the Workplace: Important Knowledge Sharing Behaviours
Anoush Margarayn,Allison Littlejohn,Colin Milligan
International Journal of Advanced Corporate Learning (iJAC) , 2011, DOI: 10.3991/ijac.v4i4.1801
Abstract: In this paper we identify a set of learning practices adopted by knowledge workers as they learn at work. We examine how key knowledge sharing behaviours: consuming, connecting, creating and contributing knowledge, are associated with these learning practices. Each learning practice brings together a combination of these components to form a distinct learning pathway, providing a baseline for rethinking combinations of practices for more effective learning and development in the workplace.
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