A model for the control mode man-computer interface dialogue

A four stage model is presented for the control mode man-computer interface dialogue. It consists of context development, semantic development syntactic development, and command execution. Each stage is discussed in terms of the operator skill levels (naive, novice, competent, and expert) and pertinent human factors issues. These issues are human problem solving, human memory, and schemata. The execution stage is discussed in terms of the operators typing skills. This model provides an understanding of the human process in command mode activity for computer systems and a foundation for relating system characteristics to operator characteristics

DSN human factors project

The project plan was to hold focus groups to identify the factors influencing the ease of use characteristics of software and to bond the problem. A questionnaire survey was conducted to evaluate those factors which were more appropriately measured with that method. The performance oriented factors were analyzed and relationships hypothesized. The hypotheses were put to test in the experimental phase of the project. In summary, the initial analysis indicates that there is an initial performance effect favoring computer controlled dialogue but the advantage fades fast as operators become experienced. The user documentation style is seen to have a significant effect on performance. The menu and prompt command formats are preferred by inexperienced operators. The short form mnemonic is least favored. There is no clear best command format but the short form mnemonic is clearly the worst

AdmixPipe v3: facilitating population structure delimitation from SNP data

Quantifying genetic clusters (=populations) from genotypic data is a fundamental, but non-trivial task for population geneticists that is compounded by: hierarchical population structure, diverse analytical methods, and complex software dependencies. AdmixPipe v3 ameliorates many of these issues in a single bioinformatic pipeline that facilitates all facets of population structure analysis by integrating outputs generated by several popular packages (i.e. CLUMPAK, EvalAdmix). The pipeline interfaces disparate software packages to parse Admixture outputs and conduct EvalAdmix analyses in the context of multimodal population structure results identified by CLUMPAK. We further streamline these tasks by packaging AdmixPipe v3 within a Docker container to create a standardized analytical environment that allows for complex analyses to be replicated by different researchers. This also grants operating system flexibility and mitigates complex software dependencies

ClineHelpR: An R Package for Genomic Cline Outlier Detection and Visualization

Background Patterns of multi-locus differentiation (i.e., genomic clines) often extend broadly across hybrid zones and their quantification can help diagnose how species boundaries are shaped by adaptive processes, both intrinsic and extrinsic. In this sense, the transitioning of loci across admixed individuals can be contrasted as a function of the genome-wide trend, in turn allowing an expansion of clinal theory across a much wider array of biodiversity. However, computational tools that serve to interpret and consequently visualize ‘genomic clines’ are limited, and users must often write custom, relatively complex code to do so. Results Here, we introduce the ClineHelpR R-package for visualizing genomic clines and detecting outlier loci using output generated by two popular software packages, bgc and Introgress. ClineHelpR bundles both input generation (i.e., filtering datasets and creating specialized file formats) and output processing (e.g., MCMC thinning and burn-in) with functions that directly facilitate interpretation and hypothesis testing. Tools are also provided for post-hoc analyses that interface with external packages such as ENMeval and RIdeogram. Conclusions Our package increases the reproducibility and accessibility of genomic cline methods, thus allowing an expanded user base and promoting these methods as mechanisms to address diverse evolutionary questions in both model and non-model organisms. Furthermore, the ClineHelpR extended functionality can evaluate genomic clines in the context of spatial and environmental features, allowing users to explore underlying processes potentially contributing to the observed patterns and helping facilitate effective conservation management strategies

The Pioneer Anomaly

Radio-metric Doppler tracking data received from the Pioneer 10 and 11 spacecraft from heliocentric distances of 20-70 AU has consistently indicated the presence of a small, anomalous, blue-shifted frequency drift uniformly changing with a rate of ~6 x 10^{-9} Hz/s. Ultimately, the drift was interpreted as a constant sunward deceleration of each particular spacecraft at the level of a_P = (8.74 +/- 1.33) x 10^{-10} m/s^2. This apparent violation of the Newton's gravitational inverse-square law has become known as the Pioneer anomaly; the nature of this anomaly remains unexplained. In this review, we summarize the current knowledge of the physical properties of the anomaly and the conditions that led to its detection and characterization. We review various mechanisms proposed to explain the anomaly and discuss the current state of efforts to determine its nature. A comprehensive new investigation of the anomalous behavior of the two Pioneers has begun recently. The new efforts rely on the much-extended set of radio-metric Doppler data for both spacecraft in conjunction with the newly available complete record of their telemetry files and a large archive of original project documentation. As the new study is yet to report its findings, this review provides the necessary background for the new results to appear in the near future. In particular, we provide a significant amount of information on the design, operations and behavior of the two Pioneers during their entire missions, including descriptions of various data formats and techniques used for their navigation and radio-science data analysis. As most of this information was recovered relatively recently, it was not used in the previous studies of the Pioneer anomaly, but it is critical for the new investigation.Comment: 165 pages, 40 figures, 16 tables; accepted for publication in Living Reviews in Relativit

Are Populations of Economically Important Bonefish and Queen Conch \u27Open\u27 or \u27Closed\u27 in the Northern Caribbean Basin?

Demographics of co-occurring species can often be diagnosed through population genomic analyses of single nucleotide polymorphisms (SNPs). These data can define population structure, gene flow, and candidate regions in the genome that potentially reflect local adaptations. They can also gauge whether populations are demographically “open” or “closed” (i.e., with global or local recruitment). We derived SNPs from double-digest restriction-site associated DNA (ddRAD) to test the demographics of commercially important bonefish Albula vulpes (N = 117) and queen conch Lobatus gigas (N = 60) from two northeast Caribbean Basin islands (Grand Bahama to the north and Eleuthera to the south). Specifically, we tested the hypothesis that the strong west-to-east current in the Great Bahama Canyon is a vicariant barrier separating the two islands. We conducted Bayesian assignment tests on putatively neutral (A. vulpes = 36,206 SNPs; L. gigas = 64,863) and highly differentiated outlier datasets (A. vulpes = 123 and 79 SNPs; L. gigas = 88 and 51, respectively). For bonefish, results diagnosed asymmetrical gene flow and north-south differentiation, as potentially driven by adult mobility and easterly currents. However, both analyses indicated genetic structure in conch, substantiating the vicariant hypothesis. These results provide templates for future research endeavors with these impacted species. Outlier loci, for example, can potentially place populations of each within a demographic continuum, rather than within a dichotomous “open/closed” framework, as well as diagnose “source” and “sink” populations, as herein. These methodologies can then be applied to co-distributed species with similar but less well-understood ecologies so as to evaluate basin-wide trends in connectivity and local adaptation

Population Connectivity in Voles (\u3ci\u3eMicrotus\u3c/i\u3e sp.) as a Gauge for Tall Grass Prairie Restoration in Midwestern North America

Ecological restoration can promote biodiversity conservation in anthropogenically fragmented habitats, but effectiveness of these management efforts need to be statistically validated to determine ’success.’ One such approach is to gauge the extent of recolonization as a measure of landscape permeability and, in turn, population connectivity. In this context, we estimated dispersal and population connectivity in prairie vole (Microtus ochrogaster; N = 231) and meadow vole (M. pennsylvanicus; N = 83) within five tall-grass prairie restoration sites embedded within the agricultural matrix of midwestern North America. We predicted that vole dispersal would be constrained by the extent of agricultural land surrounding restored habitat patches, spatially isolating vole populations and resulting in significant genetic structure. We first employed genetic assignment tests based on 15 microsatellite DNA loci to validate field-derived species-designations, then tested reclassified samples with multivariate and Bayesian clustering to assay for spatial and temporal genetic structure. Population connectivity was further evaluated by calculating pairwise FST, then potential demographic effects explored by computing migration rates, effective population size (Ne), and average relatedness (r). Genetic species assignments reclassified 25% of initial field identifications (N = 11 M. ochrogaster; N = 67 M. pennsylvanicus). In M. ochrogaster population connectivity was high across the study area, reflected in little to no spatial or temporal genetic structure. In M. pennsylvanicus genetic structure was detected, but relatedness estimates identified it as kin-clustering instead, underscoring social behavior among populations rather than spatial isolation as the cause. Estimates of Ne and r were stable across years, reflecting high dispersal and demographic resilience. Combined, these metrics suggest the agricultural matrix is highly permeable for voles and does not impede dispersal. High connectivity observed confirms that the restored landscape is productive and permeable for specific management targets such as voles and also demonstrates population genetic assays as a tool to statistically evaluate effectiveness of conservation initiatives

Acetylation Regulates WRN Catalytic Activities and Affects Base Excision DNA Repair

Background: The Werner protein (WRN), defective in the premature aging disorder Werner syndrome, participates in a number of DNA metabolic processes, and we have been interested in the possible regulation of its function in DNA repair by post-translational modifications. Acetylation mediated by histone acetyltransferases is of key interest because of its potential importance in aging, DNA repair and transcription. Methodology/Principal Findings: Here, we have investigated the p300 acetylation mediated changes on the function of WRN in base excision DNA repair (BER). We show that acetylation of WRN increases in cells treated with methyl methanesulfonate (MMS), suggesting that acetylation of WRN may play a role in response to DNA damage. This hypothesis is consistent with our findings that acetylation of WRN stimulates its catalytic activities in vitro and in vivo, and that acetylated WRN enhances pol b-mediated strand displacement DNA synthesis more than unacetylated WRN. Furthermore, we show that cellular exposure to the histone deacetylase inhibitor sodium butyrate stimulates long patch BER in wild type cells but not in WRN depleted cells, suggesting that acetylated WRN participates significantly in this process. Conclusion/Significance: Collectively, these results provide the first evidence for a specific role of p300 mediated WRN acetylation in regulating its function during BER