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

The bornavirus-derived human protein EBLN1 promotes efficient cell cycle transit, microtubule organisation and genome stability.

It was recently discovered that vertebrate genomes contain multiple endogenised nucleotide sequences derived from the non-retroviral RNA bornavirus. Strikingly, some of these elements have been evolutionary maintained as open reading frames in host genomes for over 40 million years, suggesting that some endogenised bornavirus-derived elements (EBL) might encode functional proteins. EBLN1 is one such element established through endogenisation of the bornavirus N gene (BDV N). Here, we functionally characterise human EBLN1 as a novel regulator of genome stability. Cells depleted of human EBLN1 accumulate DNA damage both under non-stressed conditions and following exogenously induced DNA damage. EBLN1-depleted cells also exhibit cell cycle abnormalities and defects in microtubule organisation as well as premature centrosome splitting, which we attribute in part, to improper localisation of the nuclear envelope protein TPR. Our data therefore reveal that human EBLN1 possesses important cellular functions within human cells, and suggest that other EBLs present within vertebrate genomes may also possess important cellular functions

CEM03 and LAQGSM03 - new modeling tools for nuclear applications

An improved version of the Cascade-Exciton Model (CEM) of nuclear reactions realized in the code CEM2k and the Los Alamos version of the Quark-Gluon String Model (LAQGSM) have been developed recently at LANL to describe reactions induced by particles and nuclei for a number of applications. Our CEM2k and LAQGSM merged with the GEM2 evaporation/fission code by Furihata have predictive powers comparable to other modern codes and describe many reactions better than other codes; therefore both our codes can be used as reliable event generators in transport codes for applications. During the last year, we have made a significant improvements to the intranuclear cascade parts of CEM2k and LAQGSM, and have extended LAQGSM to describe photonuclear reactions at energies to 10 GeV and higher. We have produced in this way improved versions of our codes, CEM03.01 and LAQGSM03.01. We present a brief description of our codes and show illustrative results obtained with CEM03.01 and LAQGSM03.01 for different reactions compared with predictions by other models, as well as examples of using our codes as modeling tools for nuclear applications.Comment: 12 pages, 10 figures, to be published in Journal of Physics: Conference Series: Proc. Europhysics Conf. on New Trends in Nuclear Physics Applications and Technologies (NPDC19), Pavia, Italy, September 5-9, 200

Survey of Pasture Species and Management, Manure Management, Milk Production and Reproduction on Pasture-Based Dairy Farms in Florida and Georgia, USA

Traditionally, most dairy farms in the south-eastern United States confine cows to barns or on pasture lots year-round and feed stored forages and concentrated feeds (Fontaneli et al. 2005). Often, much of the feed is purchased, however, the cost of purchased feed and fuel has risen rapidly in the last 5 years (NASS 2009). In addition, a significant amount of capital is tied up in buildings, machinery and manure management systems on the farms. For these reasons, many dairy farmers have shown an interest in or started transitioning to pasture-based dairy systems (Ricks and Hardee 2012). The management practices and production results of pasture-based dairy farms in the south-east appear to vary widely (Macoon et al. 2011), but have not been described. The objective of this study was to document pasture and crop management, manure management and milk production on pasture-based dairy farms in Florida and Georgia

Discovery of tissue-specific exons using comprehensive human exon microarrays

Comprehensive exon microarrays with a simple intra-gene normalization algorithm were used to detect human tissue-specific alternative splicing events, suggesting significant expression outside of known exons and well annotated genes and a high frequency of alternative splicing events

Assessing the Effects of a Program to Promote Energy-Efficiency Upgrades in Existing Homes

Energy efficient mortgages (EEMs) are intended to mitigate some of the financial barriers to upgrading the energy efficiency of existing (and sometimes new) houses. The Time of Sale Energy Renovation Program (TOSER) is designed to overcome key obstacles that have limited the use of EEMs when existing homes are sold. Conducted by Staples-Hutchinson for Pacific Gas and Electric, the Program primarily provides seminars to real estate agents and lenders to educate them about the characteristics and benefits of EEMs. EEMs typically allow the buyer to include cost-effective efficiency upgrades in her mortgage. This paper presents an overview of the TOSER Program and the results of the third and fourth evaluation of this Program. This study relied on market actor interviews and statistical analyses of key program data to identify program impacts and opportunities to improve program effectiveness

How Do Ultra‐Low Frequency Waves Access the Inner Magnetosphere During Geomagnetic Storms?

Wave‐particle interactions play a key role in radiation belt dynamics. Traditionally, ultra‐low frequency (ULF) wave‐particle interaction is parameterized statistically by a small number of controlling factors for given solar wind driving conditions or geomagnetic activity levels. Here we investigate solar wind driving of ULF wave power and the role of the magnetosphere in screening that power from penetrating deep into the inner magnetosphere. We demonstrate that during enhanced ring current intensity, the Alfvén continuum plummets, allowing lower frequency waves to penetrate deeper into the magnetosphere than during quiet periods. With this penetration, ULF wave power is able to accumulate closer to the Earth than characterized by statistical models. During periods of enhanced solar wind driving such as coronal mass ejection driven storms, where ring current intensities maximize, the observed penetration provides a simple physics‐based reason for why storm time ULF wave power is different compared to nonstorm time waves

The changing of the guard: groupwork with people who have intellectual disabilities

This paper considers the impact of service systems on group activities. It describes an inter-professional groupwork project facilitated by a social worker and a community nurse. The project provided an emancipatory experience for a group of adults who had intellectual disabilities. The group was charged with the task of reviewing and updating the recruitment and interview processes used by a 'Learning Disability Partnership Board', when employing new support workers. The paper begins with a brief history of intellectual disability and provides a context to the underpinning philosophical belief that people should be encouraged and supported to inhabit valued social roles no matter what disability they may have. It then identifies the ways in which the sponsoring health, education and social care services impacted on the creation and development of a groupwork project. It might have been expected that the nature of the intellectual disability would have been the major influence on group process. However the paper reveals that organisational constraints had a significant impact on group functioning. Issues including, staffing budgets and transport contracts impacted on group process and function. The results of the project show how, with adequate support, people with intellectual disability can make important decisions that have long-reaching impacts on the services

Alternative splicing and differential gene expression in colon cancer detected by a whole genome exon array

BACKGROUND: Alternative splicing is a mechanism for increasing protein diversity by excluding or including exons during post-transcriptional processing. Alternatively spliced proteins are particularly relevant in oncology since they may contribute to the etiology of cancer, provide selective drug targets, or serve as a marker set for cancer diagnosis. While conventional identification of splice variants generally targets individual genes, we present here a new exon-centric array (GeneChip Human Exon 1.0 ST) that allows genome-wide identification of differential splice variation, and concurrently provides a flexible and inclusive analysis of gene expression. RESULTS: We analyzed 20 paired tumor-normal colon cancer samples using a microarray designed to detect over one million putative exons that can be virtually assembled into potential gene-level transcripts according to various levels of prior supporting evidence. Analysis of high confidence (empirically supported) transcripts identified 160 differentially expressed genes, with 42 genes occupying a network impacting cell proliferation and another twenty nine genes with unknown functions. A more speculative analysis, including transcripts based solely on computational prediction, produced another 160 differentially expressed genes, three-fourths of which have no previous annotation. We also present a comparison of gene signal estimations from the Exon 1.0 ST and the U133 Plus 2.0 arrays. Novel splicing events were predicted by experimental algorithms that compare the relative contribution of each exon to the cognate transcript intensity in each tissue. The resulting candidate splice variants were validated with RT-PCR. We found nine genes that were differentially spliced between colon tumors and normal colon tissues, several of which have not been previously implicated in cancer. Top scoring candidates from our analysis were also found to substantially overlap with EST-based bioinformatic predictions of alternative splicing in cancer. CONCLUSION: Differential expression of high confidence transcripts correlated extremely well with known cancer genes and pathways, suggesting that the more speculative transcripts, largely based solely on computational prediction and mostly with no previous annotation, might be novel targets in colon cancer. Five of the identified splicing events affect mediators of cytoskeletal organization (ACTN1, VCL, CALD1, CTTN, TPM1), two affect extracellular matrix proteins (FN1, COL6A3) and another participates in integrin signaling (SLC3A2). Altogether they form a pattern of colon-cancer specific alterations that may particularly impact cell motility

Using Nutrition for Intervention and Prevention against Environmental Chemical Toxicity and Associated Diseases

BACKGROUND: Nutrition and lifestyle are well-defined modulators of chronic diseases. Poor dietary habits (such as high intake of processed foods rich in fat and low intake of fruits and vegetables), as well as a sedentary lifestyle clearly contribute to today’s compromised quality of life in the United States. It is becoming increasingly clear that nutrition can modulate the toxicity of environmental pollutants. OBJECTIVES: Our goal in this commentary is to discuss the recommendation that nutrition should be considered a necessary variable in the study of human disease associated with exposure to environmental pollutants. DISCUSSION: Certain diets can contribute to compromised health by being a source of exposure to environmental toxic pollutants. Many of these pollutants are fat soluble, and thus fatty foods often contain higher levels of persistent organics than does vegetable matter. Nutrition can dictate the lipid milieu, oxidative stress, and antioxidant status within cells. The modulation of these parameters by an individual’s nutritional status may have profound affects on biological processes, and in turn influence the effects of environmental pollutants to cause disease or dysfunction. For example, potential adverse health effects associated with exposure to polychlorinated biphenyls may increase as a result of ingestion of certain dietary fats, whereas ingestion of fruits and vegetables, rich in antioxidant and anti-inflammatory nutrients or bioactive compounds, may provide protection. CONCLUSIONS: We recommend that future directions in environmental health research explore this nutritional paradigm that incorporates a consideration of the relationships between nutrition and lifestyle, exposure to environmental toxicants, and disease. Nutritional interventions may provide the most sensible means to develop primary prevention strategies of diseases associated with many environmental toxic insults