Nominal Logic Programming

Nominal logic is an extension of first-order logic which provides a simple foundation for formalizing and reasoning about abstract syntax modulo consistent renaming of bound names (that is, alpha-equivalence). This article investigates logic programming based on nominal logic. We describe some typical nominal logic programs, and develop the model-theoretic, proof-theoretic, and operational semantics of such programs. Besides being of interest for ensuring the correct behavior of implementations, these results provide a rigorous foundation for techniques for analysis and reasoning about nominal logic programs, as we illustrate via examples.Comment: 46 pages; 19 page appendix; 13 figures. Revised journal submission as of July 23, 200

Revisiting Soil C and N Sampling: Quantitative Pits vs. Rotary Cores

Increasing atmospheric carbon dioxide and its feedbacks with global climate have sparked renewed interest in quantifying ecosystem carbon (C) budgets, including quantifying belowground pools. Belowground nutrient budgets require accurate estimates of soil mass, coarse fragment content, and nutrient concentrations. It has long been thought that the most accurate measurement of soil mass and coarse fragment content has come from excavating quantitative soil pits. However, this methodology is labor intensive and time consuming. We propose that diamond-tipped rotary cores are an acceptable if not superior alternative to quantitative soil pits for the measurement of soil mass, coarse fragment content, C and total nitrogen (N) concentrations. We tested the rotary core methodology against traditional quantitative pits at research sites in California, Nevada, and New York. We found that soil cores had 16% higher estimates of less than 2-mm soil mass than estimates obtained from quantitative pits. Conversely, soil cores had 8% lower estimates of coarse fragment mass compared with quantitative pits. There were no statistical differences in measured C or N concentrations between the two methods. At the individual site level, differences in estimates for the two methods were more pronounced, but there was no consistent tendency for cores to overestimate or underestimate a soil parameter when compared with quantitative pits

Long distance passive localization of vocalizing sei whales using an acoustic normal mode approach

Author Posting. © Acoustical Society of America, 2012. This article is posted here by permission of Acoustical Society of America for personal use, not for redistribution. The definitive version was published in Journal of the Acoustical Society of America 131 (2012): 1814-1825, doi:10.1121/1.3666015.During a 2 day period in mid-September 2006, more than 200, unconfirmed but identifiable, sei whale (Balaenoptera borealis) calls were collected as incidental data during a multidisciplinary oceanography and acoustics experiment on the shelf off New Jersey. Using a combined vertical and horizontal acoustic receiving array, sei whale movements were tracked over long distances (up to tens of kilometers) using a normal mode back propagation technique. This approach uses low-frequency, broadband passive sei whale call receptions from a single-station, two-dimensional hydrophone array to perform long distance localization and tracking by exploiting the dispersive nature of propagating normal modes in a shallow water environment. The back propagation approach is examined for accuracy and application to tracking the sei whale vocalizations identified in the vertical and horizontal array signals. This passive whale tracking, combined with the intensive oceanography measurements performed during the experiment, was also used to examine sei whale movements in relation to oceanographic features observed in this region.Office of Naval Researc

The transcription factors Ets1 and Sox10 interact during murine melanocyte development

Melanocytes, the pigment-producing cells, arise from multipotent neural crest (NC) cells during embryogenesis. Many genes required for melanocyte development were identified using mouse pigmentation mutants. The variable spotting mouse pigmentation mutant arose spontaneously at the Jackson Laboratory. We identified a G-to-A nucleotide transition in exon 3 of the Ets1 gene in variable spotting, which results in a missense G102E mutation. Homozygous variable spotting mice exhibit sporadic white spotting. Similarly, mice carrying a targeted deletion of Ets1 exhibit hypopigmentation; nevertheless, the function of Ets1 in melanocyte development is unknown. The transcription factor Ets1 is widely expressed in developing organs and tissues, including the NC. In the chick, Ets1 is required for the expression of Sox10, a transcription factor critical for the development of various NC derivatives, including melanocytes. We show that Ets1 is required early for murine NC cell and melanocyte precursor survival in vivo. Given the importance of Ets1 for Sox10 expression in the chick, we investigated a potential genetic interaction between these genes by comparing the hypopigmentation phenotypes of single and double heterozygous mice. The incidence of hypopigmentation in double heterozygotes was significantly greater than in single heterozygotes. The area of hypopigmentation in double heterozygotes was significantly larger than would be expected from the addition of the areas of hypopigmentation of single heterozygotes, suggesting that Ets1 and Sox10 interact synergistically in melanocyte development. Since Sox10 is also essential for enteric ganglia development, we examined the distal colons of Ets1 null mutants and found a significant decrease in enteric innervation, which was exacerbated by Sox10 heterozygosity. At the molecular level, Ets1 was found to activate an enhancer critical for Sox10 expression in NC-derived structures. Furthermore, enhancer activation was significantly inhibited by the variable spotting mutation. Together, these results suggest that Ets1 and Sox10 interact to promote proper melanocyte and enteric ganglia development from the NC

Density data for Lake Ontario benthic invertebrate assemblages from 1964 to 2018

Benthic invertebrates are important trophic links in aquatic food webs and serve as useful bioindicators of environmental conditions because their responses integrate the effects of both water and sediment qualities. However, long-term data sets for benthic invertebrate assemblages across broad geographic areas are rare and, even if collected, historic data sets are often not readily accessible. This data set provides densities of benthic macroinvertebrates for all taxa collected during lake-wide surveys in Lake Ontario, a Laurentian Great Lake, from 1964 to 2018. This information resulted from surveys funded by the governments of the United States and Canada to investigate the status and changes of Lake Ontario benthic community. Of the 13 lake-wide benthic surveys conducted in Lake Ontario over the course of 54 yr, we were able to acquire taxonomic data to the species level for 11 of the surveys and data to the group level for the other two surveys. Density data are provided for taxa representing the Annelida, Arthropoda, Mollusca, Cnidaria, Nemertea, and Platyhelminthes phyla. Univariate and multivariate analyses revealed that the compositional structure of Lake Ontario invertebrate assemblages differed markedly by depth and were also significantly altered by the Dreissena spp. invasion in early 1990s. The introduction of invasive dreissenids has changed the community historically dominated by Diporeia, Oligochaeta, and Sphaeriidae, to a community dominated by quagga mussels and Oligochaeta. Considering the rarity of long-term benthic data of high taxonomic resolution in lake ecosystems, this data set could be useful to explore broader aspects of ecological theory, including effects of different environmental factors and invasive species on community organization, functional and phylogenetic diversity, and spatial scale of variation in community structure. The data set could also be useful for studies on individual species including abundance and distribution, species co-occurrence, and how the patterns of dominance and rarity change over space and time. Use of this data set for academic or educational purposes is encouraged as long as the data source is properly cited using the title of this Data Paper, the names of the authors, the year of publication, the journal name, and the article number

International observational atopic dermatitis cohort to follow natural history and treatment course: TARGET-DERM AD study design and rationale

INTRODUCTION: As new topical and systemic treatments become available for atopic dermatitis (AD), there is a need to understand how treatments are being used in routine clinical practice, their comparative effectiveness and their long-term safety in diverse clinical settings. METHODS AND ANALYSIS: The TARGET-DERM AD cohort is a longitudinal, observational study of patients with AD of all ages, designed to provide practical information on long-term effectiveness and safety unobtainable in traditional registration trials. Patients with physician-diagnosed AD receiving prescription treatment (topical or systemic) will be enrolled at academic and community clinical centres. Up to 3 years of retrospective medical records, 5 years of prospective medical records, and optional biological samples and patient-reported outcomes will be collected. The primary aims include characterisation of AD treatment regimens, evaluation of response to therapy, and description of adverse events. ETHICS AND DISSEMINATION: TARGET-DERM has been approved by a central IRB (Copernicus Group IRB, 5000 Centregreen Way Suite 200, Cary, North Carolina 27513) as well as local and institutional IRBs. No additional Ethics Committee reviews. Results will be reviewed by a publications committee and submitted to peer-reviewed journals. TRIAL REGISTRATION NUMBER: NCT03661866, pre-results

What is a return to work after stroke?: 12 month work outcomes in a feasibility trial

Background: Return to work (RTW) is an outcome in determining the effectiveness of rehabilitation post-stroke. However, stroke survivors (SS) may return to different roles with altered work status. Income, hours, responsibilities and job-satisfaction may be reduced. SS may be dissatisfied if unable to resume apriori work status; alternatively adjusted work status may be viewed positively if perceived as a way of reducing the risk of another stroke. The purpose of this study was to explore what is meant by RTW. Method: Information about the nature of RTW (job type, hours, roles, responsibilities) was extracted from 3, 6 and 12 month follow-up postal questionnaires in 46 SS participants in a feasibility randomised controlled trial investigating effectiveness of a vocational rehabilitation intervention. Results/Findings: Participants took a mean 90 (SD:70, range 7-227) days to RTW. 19/46 reported working at 12 months. In 17 who supplied complete data, 7(41%) reported reduced working hours. Participants incurred a mean wage loss of 44% against pre-stroke earnings. 10/17(59%) participants were in the same job with the same employer and 6(35%) were working in different/modified jobs (1 missing:). 10/17(59%) had work-place adjustments. 18/46 (39%) participants were happy with their work situation. Discussion: Participants experienced marked changes in work status post-stroke, with implications for job-satisfaction, financial security and quality of life. Research into psychological adjustment following altered vocational status in SS is warranted. Conclusion: RTW is a complex outcome and may not translate to a return to pre-stroke vocational status. It is important to consider what constitutes a RTW following stroke

Inhibition of SIRT1 Reactivates Silenced Cancer Genes without Loss of Promoter DNA Hypermethylation

The class III histone deactylase (HDAC), SIRT1, has cancer relevance because it regulates lifespan in multiple organisms, down-regulates p53 function through deacetylation, and is linked to polycomb gene silencing in Drosophila. However, it has not been reported to mediate heterochromatin formation or heritable silencing for endogenous mammalian genes. Herein, we show that SIRT1 localizes to promoters of several aberrantly silenced tumor suppressor genes (TSGs) in which 5′ CpG islands are densely hypermethylated, but not to these same promoters in cell lines in which the promoters are not hypermethylated and the genes are expressed. Heretofore, only type I and II HDACs, through deactylation of lysines 9 and 14 of histone H3 (H3-K9 and H3-K14, respectively), had been tied to the above TSG silencing. However, inhibition of these enzymes alone fails to re-activate the genes unless DNA methylation is first inhibited. In contrast, inhibition of SIRT1 by pharmacologic, dominant negative, and siRNA (small interfering RNA)–mediated inhibition in breast and colon cancer cells causes increased H4-K16 and H3-K9 acetylation at endogenous promoters and gene re-expression despite full retention of promoter DNA hypermethylation. Furthermore, SIRT1 inhibition affects key phenotypic aspects of cancer cells. We thus have identified a new component of epigenetic TSG silencing that may potentially link some epigenetic changes associated with aging with those found in cancer, and provide new directions for therapeutically targeting these important genes for re-expression

Effects of Coping Skills Training on Quality of Life, Disease Biomarkers and Clinical Outcomes in Patients with Heart Failure: A Randomized Clinical Trial

Heart failure (HF) is a chronic disease that compromises patients’ quality of life (QoL). Interventions designed to reduce distress and improve disease self-management are needed. We evaluated the efficacy of a telephone-based coping skills training (CST) intervention