Scaffolder - Software for Reproducible Genome Scaffolding.

Background: Assembly of short-read sequencing data can result in a fragmented non-contiguous series of genomic sequences. Therefore a common step in a genome project is to join neighboring sequence regions together and fill gaps in the assembly using additional sequences. This scaffolding step, however, is non-trivial and requires manually editing large blocks of nucleotide sequence. Joining these sequences together also hides the source of each region in the final genome sequence. Taken together, these considerations may make reproducing or editing an existing genome build difficult.

Methods: The software outlined here, “Scaffolder,” is implemented in the Ruby programming language and can be installed via the RubyGems software management system. Genome scaffolds are defined using YAML - a data format, which is both human and machine-readable. Command line binaries and extensive documentation are available.

Results: This software allows a genome build to be defined in terms of the constituent sequences using a relatively simple syntax to define the scaffold. This syntax further allows unknown regions to be defined, and adds additional sequences to fill gaps in the scaffold. Defining the genome construction in a file makes the scaffolding process reproducible and easier to edit compared with FASTA nucleotide sequence.

Conclusions: Scaffolder is easy-to-use genome scaffolding software. This tool promotes reproducibility and continuous development in a genome project. Scaffolder can be found at http://next.gs

New Results for Domineering from Combinatorial Game Theory Endgame Databases

We have constructed endgame databases for all single-component positions up to 15 squares for Domineering, filled with exact Combinatorial Game Theory (CGT) values in canonical form. The most important findings are as follows. First, as an extension of Conway's [8] famous Bridge Splitting Theorem for Domineering, we state and prove another theorem, dubbed the Bridge Destroying Theorem for Domineering. Together these two theorems prove very powerful in determining the CGT values of large positions as the sum of the values of smaller fragments, but also to compose larger positions with specified values from smaller fragments. Using the theorems, we then prove that for any dyadic rational number there exist Domineering positions with that value. Second, we investigate Domineering positions with infinitesimal CGT values, in particular ups and downs, tinies and minies, and nimbers. In the databases we find many positions with single or double up and down values, but no ups and downs with higher multitudes. However, we prove that such single-component ups and downs easily can be constructed. Further, we find Domineering positions with 11 different tinies and minies values. For each we give an example. Next, for nimbers we find many Domineering positions with values up to *3. This is surprising, since Drummond-Cole [10] suspected that no *2 and *3 positions in standard Domineering would exist. We show and characterize many *2 and *3 positions. Finally, we give some Domineering positions with values interesting for other reasons. Third, we have investigated the temperature of all positions in our databases. There appears to be exactly one position with temperature 2 (as already found before) and no positions with temperature larger than 2. This supports Berlekamp's conjecture that 2 is the highest possible temperature in Domineering

An "All Hands" Call to the Social Science Community: Establishing a Community Framework for Complexity Modeling Using Agent Based Models and Cyberinfrastructure

To date, many communities of practice (COP) in the social sciences have been struggling with how to deal with rapidly growing bodies of information. Many CoPs across broad disciplines have turned to community frameworks for complexity modeling (CFCMs) but this strategy has been slow to be discussed let alone adopted by the social sciences communities of practice (SS-CoPs). In this paper we urge the SS-CoPs that it is timely to develop and establish a CBCF for the social sciences for two major reasons: the rapid acquisition of data and the emergence of critical cybertools which can facilitate agent-based, spatially-explicit models. The goal of this paper is not to prescribe how a CFCM might be set up but to suggest of what components it might consist and what its advantages would be. Agent based models serve the establishment of a CFCM because they allow robust and diverse inputs and are amenable to output-driven modifications. In other words, as phenomena are resolved by a SS-CoP it is possible to adjust and refine ABMs (and their predictive ability) as a recursive and collective process. Existing and emerging cybertools such as computer networks, digital data collections and advances in programming languages mean the SS-CoP must now carefully consider committing the human organization to enabling a cyberinfrastructure tool. The combination of technologies with human interfaces can allow scenarios to be incorporated through 'if' 'then' rules and provide a powerful basis for addressing the dynamics of coupled and complex social ecological systems (cSESs). The need for social scientists to be more engaged participants in the growing challenges of characterizing chaotic, self-organizing social systems and predicting emergent patterns makes the application of ABMs timely. The enabling of a SS-CoP CFCM human-cyberinfrastructure represents an unprecedented opportunity to synthesize, compare and evaluate diverse sociological phenomena as a cohesive and recursive community-driven process.Community-Based Complex Models, Mathematics, Social Sciences

A Study of the Effectiveness of Selected Aspects of the Developmental Education Program at an Urban Multicampus Community College

The purpose of this study was to examine the effectiveness of developmental/remedial education at an urban multi-campus community college. The study sought (1) to identify the number and demographic characteristics of students served by developmental studies, (2) to determine the academic achievement and persistence of these students, and (3) to assess the performance of developmental English students in regular college English. Data were obtained for a two year period on all new students who enrolled in the fall of 1980. The study employed two approaches: (1) a descriptive analysis of the variables of age, sex, race, enrollment status and day/night attendance; (2) a static group comparison to detect differences in performance in college English, in cumulative grade point average, in credits completed and in the number of quarters attended between developmental and other students. The descriptive analysis revealed that (1) slightly more than one-fourth of new students enrolled in a developmental course; (2) developmental students were likely to be younger, male, and to attend full-time during the day; and (3) the large majority of developmental students was white, although non-whites were overrepresented. Full-time developmental students were found to complege as many quarters of enrollment as other full-time students and part-time developmental students completed a significantly higher number of quarters than did part-time nondevelopmental students. Developmental students\u27 mean GPA was significantly lower than the GPA of others. When examined by increasing intervals of credits earned, however, developmental students\u27 GPA increased in linear fashion and eventually surpassed that of nondevelopmental students. For students enrolled in more than one developmental course this pattern was not obtained. An inverse relationship was found between the number of developmental courses and grade point average. Students who completed a developmental English course performed less well in college English than other students, yet a substantial majority (68 percent) was able to pass the course with at least a grade of C. Overall, the findings of this study indicate that developmental students remain in school as long as, and eventually perform as well as, other students

MA

thesisThe external branch of the superior laryngeal nerve (ESLN) innervates the cricothyroid (CT) muscle of the larynx, a vocal fold tensor primarily responsible for pitch elevation. For over 100 years, a controversy has existed regarding the laryngeal signs that should be considered pathognomonic of unilateral ESLN paralysis. Regrettably, little progress has been made in resolving this controversy, as the extant clinical literature is characterized by contradiction and inconsistency. Myriad descriptions exist of the laryngeal behaviors ostensibly associated with unilateral ESLN denervation. To address this longstanding controversy and improve diagnostic precision, this preliminary investigation aimed to model "in vivo" acute, unilateral CT dysfunction by temporarily blocking the ESLN using lidocaine hydrochloride (HCL), and verifying selective denervation using laryngeal electromyography (LEMG). The purpose of this investigation was twofold: (1) to identify the salient laryngeal features associated with acute denervation (i.e., the pathognomonic features of unilateral CT dysfunction), and (2) to identify a set of laryngeal tasks that maximally provoke or reveal ESLN dysfunction, thereby contributing to a set of diagnostic tasks/markers that will improve diagnostic accuracy during clinical assessment. Ten vocally normal adult males (mean age = 25 yrs.; range = 19 to 29 years) underwent lidocaine block of the right ESLN, and flexible videolaryngostroboscopic (FVLS) recordings were acquired before and during the block. Eleven blinded, expert judges (6 laryngologists and 5 Ph.D. speech-language pathologists) rated randomized, pre- vs. during-block recordings of 10 vocal tasks using standard FVLS rating protocols. Contrary to clinical reports, no evidence of hypomobility/sluggishness of the ipsilateral vocal fold, or a reliable pattern of axial rotation of the larynx during high pitch voice was observed. Furthermore, no evidence was observed to support reduced vocal fold longitudinal tension, aryepiglottic fold length asymmetry, phase asymmetry, vocal fold plane differences, or glottic insufficiency, as diagnostic features of unilateral CT dysfunction. Instead, the analysis revealed (1) a pattern of deviation of the petiole of the epiglottis to the side of weakness (i.e., the right) in 60% of participants during a glissando up maneuver produced at normal volume, and (2) a pattern of axial rotation of the posterior commissure to the left and the anterior commissure to right in 50% of participants during a maneuver which rapidly alternated between a maximum vocal fold abduction task (Sniff) and a high-pitched "ee" production. Both of these findings have not been previously reported elsewhere, and potentially represent new diagnostic markers of unilateral CT paralysis. The results are discussed with respect to their clinical implications, and the necessity to explore both females and clinical populations to better appreciate the clinical utility of these diagnostic signs

Land O' Lakes

The case begins with an examination of Land O' Lakes' diversified portfolio of businesses. The business had undergone significant changes since 1998 - it dominated market share in butter and deli cheese, had become the largest crop protection, plant nutrient, and feed manufacturer in the US, and was the fourth largest US seed company. Land O'Lakes used mergers, joint ventures, acquisitions of public and private firms, and divestitures/closing of assets to restructure its portfolio to build its portfolio. The main issue was to evaluate its diversified portfolio of businesses and find ways to improve future performance.Dairy, Agribusiness, Portfolio, Cooperative, Agribusiness, Livestock Production/Industries,

An analysis of fiscal allocations in elementary schools meeting and not meeting Ayp

This study used a sequential explanatory, mixed-methods design to explore the relationship between fiscal decision making and the school improvement planning process at school sites in a large, southwestern school district and the impact those decisions and decision-making processes may have had on student achievement outcomes in elementary schools; The methodology for the study is comprised of two research phases. Phase I included a quantitative analysis of elementary school expenditure patterns across those categories delineated in the Cooper\u27s and Lybrand\u27s Finance Analysis Model databank for a large urban district in the southwest. Comparisons were made across three sub-groups of elementary schools: (1) those schools meeting Adequate Yearly Progress (AYP), (2) those schools on the Watch List, and (3) those schools delineated as In Need of Improvement, as defined by the state\u27s accountability plan for the No Child Left Behind Act. Phase II consisted of a qualitative analysis of school fiscal decision making through a series of case studies. Six schools, two from each subgroup with similar demographic characteristics, were studied; Several researchers have made the study of school-based expenditures a priority in recent years; however, the literature in school finance has mostly concentrated on examining district or state expenditure patterns. This study focused on the former and intended to reveal how school-based fiscal decisions are, or are not, related to the school improvement planning process; The major findings of the study included determining that school improvement was an ongoing dynamic process, and fiscal decisions were, in fact, tied to strategic academic goals in elementary schools exhibiting progress. The two functions, school improvement and fiscal decision making, did, however, occur in isolation in most instances. As a result, a limited connection existed between the two entities; Providing information to education leaders on how schools spend their money, how they arrive at those decisions, and how those decisions are, or are not, related to school improvement efforts may assist districts in developing a better understanding of the relationship between fiscal decision making and school improvement efforts, and, ultimately, their impact on student achievement outcomes.*; *This dissertation is a compound document (contains both a paper copy and a CD as part of the dissertation). The CD requires the following system requirements: Microsoft Office

Current Challenges in Financing Agricultural Cooperatives

Agricultural, Cooperatives, Finance, Agribusiness, L10, L23, L16, Q13,