Self-Admitted Technical Debt - An Investigation from Farm to Table to Refactoring

Self-Admitted Technical Debt (SATD) is a metaphorical concept which describes the self-documented contribution of technical debt to a software project in the manner of source-code comments. SATD can linger in projects and degrade source-code quality, but its palpable visibility draws a peculiar sort of attention from developers. There is a need to understand the significance of engineering SATD within a software project, as these debts may have lurking repercussions. While the oft-performed action of refactoring may work against a generalized volume of source code degradation, there exists only slight evidence suggesting that the act of refactoring has a distinct impact on SATD. In fact, refactoring is better understood to convalesce the measurable quality of source code which may very well remain unimpressed by the preponderance of SATD instances. In observation of the cross-section of these two concepts, it would seem logical to presume some magnitude of correlation between refactorings and SATD removals. In this thesis, we will address the extent of such concurrence, while also seeking to develop a dependable tool to promote the empirical studies of SATD. Using this tool, we mined data from 5 open source Java projects, from which associations between SATD removals and refactoring actions were drawn to show that developers tend to refactor SATD-containing code differently than they do code elsewhere in their projects. We also concluded that design-related SATD is more likely to entail a refactoring than non-design SATD

SATDBailiff- Mining and Tracking Self-Admitted Technical Debt

Self-Admitted Technical Debt (SATD) is a metaphorical concept to describe the self-documented addition of technical debt to a software project in the form of source code comments. SATD can linger in projects and degrade source-code quality, but it can also be more visible than unintentionally added or undocumented technical debt. Understanding the implications of adding SATD to a software project is important because developers can benefit from a better understanding of the quality trade-offs they are making. However, empirical studies, analyzing the survivability and removal of SATD comments, are challenged by potential code changes or SATD comment updates that may interfere with properly tracking their appearance, existence, and removal. In this paper, we propose SATDBailiff, a tool that uses an existing state-of-the-art SATD detection tool, to identify SATD in method comments, then properly track their lifespan. SATDBailiff is given as input links to open source projects, and its output is a list of all identified SATDs, and for each detected SATD, SATDBailiff reports all its associated changes, including any updates to its text, all the way to reporting its removal. The goal of SATDBailiff is to aid researchers and practitioners in better tracking SATDs instances, and providing them with a reliable tool that can be easily extended. SATDBailiff was validated using a dataset of previously detected and manually validated SATD instances. SATDBailiff is publicly available as an open source, along with the manual analysis of SATD instances associated with its validation, on the project website

Four Linked Genes Participate in Controlling Sporulation Efficiency in Budding Yeast

Quantitative traits are conditioned by several genetic determinants. Since such genes influence many important complex traits in various organisms, the identification of quantitative trait loci (QTLs) is of major interest, but still encounters serious difficulties. We detected four linked genes within one QTL, which participate in controlling sporulation efficiency in Saccharomyces cerevisiae. Following the identification of single nucleotide polymorphisms by comparing the sequences of 145 genes between the parental strains SK1 and S288c, we analyzed the segregating progeny of the cross between them. Through reciprocal hemizygosity analysis, four genes, RAS2, PMS1, SWS2, and FKH2, located in a region of 60 kilobases on Chromosome 14, were found to be associated with sporulation efficiency. Three of the four “high” sporulation alleles are derived from the “low” sporulating strain. Two of these sporulation-related genes were verified through allele replacements. For RAS2, the causative variation was suggested to be a single nucleotide difference in the upstream region of the gene. This quantitative trait nucleotide accounts for sporulation variability among a set of ten closely related winery yeast strains. Our results provide a detailed view of genetic complexity in one “QTL region” that controls a quantitative trait and reports a single nucleotide polymorphism-trait association in wild strains. Moreover, these findings have implications on QTL identification in higher eukaryotes

A phase I study of CPI-613 (devimistat) in combination with chemoradiation in patients with pancreatic adenocarcinoma

Background: Local tumor progression is a cause of significant mortality and morbidity in patients with unresectable pancreatic ductal adenocarcinoma (PDAC). Effective approaches to achieve durable local control are urgently needed. Metabolic reprogramming and enhanced mitochondrial function, both hallmarks of PDAC, are known contributors to chemo- and radio-resistance. CPI-613, a lipoic acid analog that selectively inhibits components of the Krebs cycle in tumors, showed promising preclinical synergy in combination with gemcitabine and radiation therapy (gem-RT). Methods: We describe a single-arm, single-center, open-label, phase I study designed to determine the maximumtolerated dose of CPI-613 when used concomitantly with gemcitabine and intensity modulated radiation therapy (IMRT) for local control of PDAC. CPI-613 will be administered once weekly by intravenous infusion over approximately 2 hours at a starting dose of 500 mg/m2 and dose-escalated/de-escalated using a Bayesian optimal interval design. Gemcitabine will be given once weekly at 400 mg/m2 dosage and IMRT as 54 Gray (Gy) in 30 fractions (1.8 Gy per fraction) with five fractions given per week. Up to 24 patients will be enrolled for the study after meeting the following main eligibility criteria, which include: pathologically confirmed PDAC; inoperable disease that by institutional pancreatic multidisciplinary tumor board or multidisciplinary review are considered to benefit from definitive local control of the primary tumor; ECOG of 0-2; and adequate organ and marrow function after completion of intended systemic chemotherapy. The secondary objectives are to determine the recommended phase II dose of CPI-613 when used with gem-RT, safety and tolerability of CPI-613-gem-RT, overall survival, local progression-free survival (PFS), overall PFS, patient-reported quality of life after treatment, and late gastrointestinal toxicities following treatment with CPI-613-gem-RT

Arabidopsis CULLIN3 Genes Regulate Primary Root Growth and Patterning by Ethylene-Dependent and -Independent Mechanisms

CULLIN3 (CUL3) together with BTB-domain proteins form a class of Cullin-RING ubiquitin ligases (called CRL3s) that control the rapid and selective degradation of important regulatory proteins in all eukaryotes. Here, we report that in the model plant Arabidopsis thaliana, CUL3 regulates plant growth and development, not only during embryogenesis but also at post-embryonic stages. First, we show that CUL3 modulates the emission of ethylene, a gaseous plant hormone that is an important growth regulator. A CUL3 hypomorphic mutant accumulates ACS5, the rate-limiting enzyme in ethylene biosynthesis and as a consequence exhibits a constitutive ethylene response. Second, we provide evidence that CUL3 regulates primary root growth by a novel ethylene-dependant pathway. In particular, we show that CUL3 knockdown inhibits primary root growth by reducing root meristem size and cell number. This phenotype is suppressed by ethylene-insensitive or resistant mutations. Finally, we identify a function of CUL3 in distal root patterning, by a mechanism that is independent of ethylene. Thus, our work highlights that CUL3 is essential for the normal division and organisation of the root stem cell niche and columella root cap cells

Bermudagrass Cultivar Trial Subjected to Simulated Athletic Field Traffic

Interest in bermudagrass use as an athletic field playing surface has grown recently with the release of more cold tolerant cultivars of bermudagrass. Bermudagrass is more traffic tolerant than Kentucky bluegrass in many situations. It also performs better during the summer months due to the C4 photosynthesis pathways compared with the C3 pathways of Kentucky bluegrass. For these reasons, many Iowa athletic field managers are curious about the performance of bermudagrass as an athletic field playing surface in Iowa. The objectives of this study were to compare the performance and traffic tolerance of cold tolerant bermudagrass cultivars with a simulated Iowa high school football traffic season. This is the first year of a two-year study.</p

Kentucky Bluegrass Shade Cultivar Evaluation Trial

This is the initial establishment data from Kentucky bluegrass growing in natural shade conditions. This is a National Turfgrass Evaluation Program (NTEP) ancillary trial, and is being conducted at several research stations in the United States. It contains 89 seeded cultivars, including a number of new experimental cultivars. Iowa State is conducting both a sun and shade setting of this trial.</p

Amended Topdressing for Aerification Recovery

Core aerification is an effective cultivation practice utilized by most golf courses for thatch management and soil compaction reduction. Timely recovery of aerification cultural practices is an important management consideration for golf course superintendents. Quick recovery periods are preferred by course owners/greens committees to reduce loss of revenue and by golfers/members to reduce loss of fall playing time. Filling aerification holes and sand topdressing after aerification can speed recovery, but it is often still days before the playing surface is returned to optimal condition. Because the many benefits of core aeration outweigh the disruption of playing conditions, cultural practice improvements to decrease recovery time are necessary.</p

Effects of Wetting Agent Timing on Sand-Capped Athletic Fields

Athletic field playability and safety is a growing national concern, particularly at the high school sports level. Athletic field usage rates increase each year while field maintenance budgets are stagnant, if not reduced. Research is needed on improving cultural practices to maximize playability and safety of natural grass athletic fields, especially in reference to prolonging field surface integrity throughout the extended high school football season. Many athletic fields endure multiple practices and games per week. Despite weather-related conditions detrimental to field integrity, Friday night games cannot be rescheduled and practice field availability often is lacking. The objective of this trial is to investigate the use of wetting agent products and application timings as part of a sand-capped natural grass athletic field management plan to improve rootzone water content management. Multiple types of wetting agents and two application timings/rates were tested to determine product methodology and efficacy.</p