OPTIMAL SUPPLEMENTAL COVERAGE OPTION CROP INSURANCE DECISION FOR KENTUCKY COMMODITY CROP PRODUCERS

The 2018 Farm Bill has reopened commodity program enrollment for producers, and thus renewed interest in the Supplemental Coverage Option (SCO) of the Federal Crop Insurance Program (FCIP). This thesis examines the potential risk management benefits afforded to Kentucky corn, soybean and wheat producers by the SCO. A simulation model is used to rank downside-risk minimization of the common Multi-peril Crop Insurance Policies (MPCI) policies both with and without the SCO for various farm-level yield risk and farm- to SCO area-level yield correlations. The study found that the SCO endorsement was a component of every optimal insurance choice for all possible combinations examined in this study. Soybeans had the greatest homogeneity, while wheat had the greatest variability in optimal insurance choice. The results show that the SCO should enter into a producer\u27s crop insurance decision and also commodity program enrollment decision — when applicable. The yearly commodity program enrollment deadlines occurring throughout the life of the current Farm Bill make this study especially timely

Sets of lines and cutting out polyhedral objects

AbstractWe study algorithmic questions related to cutting polyhedral shapes with a hot wire cutter. Such cutters are popular manufacturing tools for cutting expanded polystyrene (styrofoam) with a thin, moving heated wire. In particular, we study the question of polyhedral-wise continuity: Can a given object be cut out without disconnecting and then reattaching the wire? In an abstract setting this question translates to properties of sets of lines and segments and therefore becomes suitable for computational geometry techniques. On the combinatorial and algorithmic levels the results and methods are related to two problems: (1) given a set F={f1,…,fk} of polygons and a polygon f, decide if there is a subset of lines in the set of lines not stabbing F that cover f; (2) construct the connectivity graph for free movements of lines that maintain contact with the polyhedral shape. Problem (1) is solved with the dual projection and arrangements of convex and concave x-monotone curves. Problem (2) can be solved with a combination of the skewed projections [6] and hyperbola arrangements proposed by McKenna and O'Rourke [11]. We provide an O(n5) algorithm for constructing a cutting path, if it exists. The complexity of the algorithm is determined by the O(n4) size of the connectivity graph and the cost of solving (2)

Statistical Phylogenetic Tree Analysis Using Differences of Means

We propose a statistical method to test whether two phylogenetic trees with given alignments are significantly incongruent. Our method compares the two distributions of phylogenetic trees given by the input alignments, instead of comparing point estimations of trees. This statistical approach can be applied to gene tree analysis for example, detecting unusual events in genome evolution such as horizontal gene transfer and reshuffling. Our method uses difference of means to compare two distributions of trees, after embedding trees in a vector space. Bootstrapping alignment columns can then be applied to obtain p-values. To compute distances between means, we employ a "kernel trick" which speeds up distance calculations when trees are embedded in a high-dimensional feature space, e.g. splits or quartets feature space. In this pilot study, first we test our statistical method's ability to distinguish between sets of gene trees generated under coalescence models with species trees of varying dissimilarity. We follow our simulation results with applications to various data sets of gophers and lice, grasses and their endophytes, and different fungal genes from the same genome. A companion toolkit, {\tt Phylotree}, is provided to facilitate computational experiments.Comment: 17 pages, 6 figure

Non-Transgenic CRISPR-Mediated Knockout of Entire Ergot Alkaloid Gene Clusters in Slow-Growing Asexual Polyploid Fungi

The Epichloë species of fungi include seed-borne symbionts (endophytes) of cool-season grasses that enhance plant fitness, although some also produce alkaloids that are toxic to livestock. Selected or mutated toxin-free endophytes can be introduced into forage cultivars for improved livestock performance. Long-read genome sequencing revealed clusters of ergot alkaloid biosynthesis (EAS) genes in Epichloë coenophiala strain e19 from tall fescue (Lolium arundinaceum) and Epichloë hybrida Lp1 from perennial ryegrass (Lolium perenne). The two homeologous clusters in E. coenophiala—a triploid hybrid species—were 196 kb (EAS1) and 75 kb (EAS2), and the E. hybrida EAS cluster was 83 kb. As a CRISPR-based approach to target these clusters, the fungi were transformed with ribonucleoprotein (RNP) complexes of modified Cas9 nuclease (Cas9-2NLS) and pairs of single guide RNAs (sgRNAs), plus a transiently selected plasmid. In E. coenophiala, the procedure generated deletions of EAS1 and EAS2 separately, as well as both clusters simultaneously. The technique also gave deletions of the EAS cluster in E. hybrida and of individual alkaloid biosynthesis genes (dmaW and lolC) that had previously proved difficult to delete in E. coenophiala. Thus, this facile CRISPR RNP approach readily generates non-transgenic endophytes without toxin genes for use in research and forage cultivar improvement

Experimenting with database segmentation size vs time performance for mpiBLAST on an IBM HS21 blade cluster

Large-scale genomic projects such as the Epichloë festucae Genome Project require regular use of bioinformatic tools. When using BLAST in conjunction with larger databases, processing complex sequences often uses substantial computation time. Parallelization is considered a standard method of curbing extensive computing requirements and parallel implementations of BLAST, such as mpiBLAST, are freely available

MedSurv: a software application for creating, conducting and managing medical surveys and questionnaires

MedSurv is a system designed for the rapid creation and maintenance of research surveys and questionnaires that does not require programmer intervention. MedSurv is built with medical surveys in mind and utilizes a group-based permission control with additional security features to help ensure compliance with applicable healthcare regulations. MedSurv is designed as a module for DotNetNuke [1], an open source portal and content management system built with ASP.Net technology, and therefore can be deployed and managed as intranet, extranet, and web sites. At the same time, all data is stored at the researcher\u27s institution to guarantee the required data privacy. Thanks to its built-in support for user authentication and user roles, there is no need to create such functionality from scratch. However, a group-based permissions system is added to MedSurv to support sufficient granularity for access control. Although from the data access point of view data storage acts as a relational table, MedSurv uses a solution that we call virtual tables. The premise behind such a solution is that the structure of the tables is itself stored in a set of relational tables within the database, essentially creating a miniature database within the database. This additional layer is transparent to the user and removes the need for any programming or database knowledge. At the same time it gives the user the flexibility of changing the survey at runtime. Unlike a traditional structure that may require database developer\u27s involvement each time a survey is added or changed, with virtual tables there is very low developer and database administration need after launch. MedSurv allows for creating complex medical surveys and is, in particular, used to develop questionnaires for research driven data collection in the Department of Gastroenterology

Spatially-distributed coverage optimization and control with limited-range interactions

This paper presents coordination algorithms for groups of mobile agents performing deployment and coverage tasks. As an important modeling constraint, we assume that each mobile agent has a limited sensing/communication radius. Based on the geometry of Voronoi partitions and proximity graphs, we analyze a class of aggregate objective functions and propose coverage algorithms in continuous and discrete time. These algorithms have convergence guarantees and are spatially distributed with respect to appropriate proximity graphs. Numerical simulations illustrate the results.Comment: 31 pages, some figures left out because of size limits. Complete preprint version available at http://motion.csl.uiuc.ed

\u3cem\u3ePhylotree\u3c/em\u3e – a toolkit for computing experiments with distance-based methods for genome coevolution

We have developed software called Phylotree as a toolkit for running experiments to study gene cophylogenies for genome evolution using distance-based methods. In particular, the toolkit has been instrumental in conducting processing-heavy experiments with the new “difference of means” statistical method. Phylotree was used to run experiments using simulated data as well as biological sequences of well known host and parasite species, and is distributed with data and configuration files allowing these experiments to be reproduced

Phylotree – a toolkit for computing experiments with distance-based methods for genome coevolution

We have developed software called Phylotree as a toolkit for running experiments to study gene cophylogenies for genome evolution using distance-based methods. In particular, the toolkit has been instrumental in conducting processing-heavy experiments with the new “difference of means” statistical method. Phylotree was used to run experiments using simulated data as well as biological sequences of well known host and parasite species, and is distributed with data and configuration files allowing these experiments to be reproduced

Automating Deployment of Several GBrowse Instances

Background As part of the fungal endophyte genomes project, we maintain genome browsers for several dozen strains of fungi from the Clavicipitaceae and related families. These genome browsers are based on the GBrowse software, with a large collection of in-house software for visualization, analysis, and searching of genome features. Although GBrowse supports serving multiple data sources, such as distinct genome assemblies, from a single GBrowse instance, there are advantages to maintaining separate instances for each genome. Besides permitting per-genome customizations of the software, page layout, and database schemas, our use of separate instances also allows us to maintain different security and password requirements for genomes in different stages of publication. Materials and methods We have developed a suite of software for deploying and maintaining a large collection of GBrowse instances. This software, a combination of Perl, shell libraries, and scripts, automates the process of deploying the software, databases, and configuration required to make a new customized genome browser available online; and furthermore automates loading each instance’s database with genome sequences, annotations, and other data. To maintain a mostly synchronized codebase while allowing distinct configuration, we record each instance’s software and configuration as a branch in a Subversion version control repository. This use of version control ensures that bug fixes and software improvements are easily applied to each relevant instance, without losing customizations. Results We describe the components of our genome browser instances, the design and implementation of our deployment software, and various challenges and practical considerations we have encountered while using this software to maintain genome browsers for nearly fifty organism strains and assembly versions