MMpred: functional miRNA – mRNA interaction analyses by miRNA expression prediction

Background: MicroRNA (miRNA) directed gene repression is an important mechanism of posttranscriptional regulation. Comprehensive analyses of how microRNA influence biological processes requires paired miRNA-mRNA expression datasets. However, a review of both GEO and ArrayExpress repositories revealed few such datasets, which was in stark contrast to the large number of messenger RNA (mRNA) only datasets. It is of interest that numerous primary miRNAs (precursors of microRNA) are known to be co-expressed with coding genes (host genes). Results: We developed a miRNA-mRNA interaction analyses pipeline. The proposed solution is based on two miRNA expression prediction methods – a scaling function and a linear model. Additionally, miRNA-mRNA anticorrelation analyses are used to determine the most probable miRNA gene targets (i.e. the differentially expressed genes under the influence of up- or down-regulated microRNA). Both the consistency and accuracy of the prediction method is ensured by the application of stringent statistical methods. Finally, the predicted targets are subjected to functional enrichment analyses including GO, KEGG and DO, to better understand the predicted interactions. Conclusions: The MMpred pipeline requires only mRNA expression data as input and is independent of third party miRNA target prediction methods. The method passed extensive numerical validation based on the binding energy between the mature miRNA and 3’ UTR region of the target gene. We report that MMpred is capable of generating results similar to that obtained using paired datasets. For the reported test cases we generated consistent output and predicted biological relationships that will help formulate further testable hypotheses

Onboard sampling of the rockfish and lingcod commerical passenger fishing vessel industry in northern and central California, 1992

In 1992 fishery technicians sampled 230 commercial passenger fishing vessel (CPFV) trips targeting rockfish and lingcod from the port areas of Fort Bragg, Bodega Bay, San Francisco, Monterey, and Morro Bay. The skippers of 44 vessels, and 2,190 anglers, cooperated in the study. Species composition by port area and month, catch-per-unit-effort, mean length, and length frequency of lingcod and the 18 most frequently observed rockfish species are presented, as well as fishing effort relative to time, depth, and distance from port. Total catch estimates based on unadjusted and adjusted logbook records are summarized. Average catch of kept fish per angler day was 12.6 and average catch of kept fish per angler hour was 4.0. A continuing trend of an increasing frequency of trips to deep (> 40 fm) locations was observed in the Bodega Bay, San Francisco, and Monterey areas. Bodega Bay and San Francisco showed the highest frequency of trips to distant locations. Sixty species comprised of 29,731 fish were observed caught during the study. Rockfish comprised 93.5% by number of the total observed catch. The five most frequently observed species were blue, yellowtail, widow and rosy rockfishes, and bocaccio, with lingcod ranking eighth. CPFV angler success, as determined by catch per angler hour, generally increased in all ports in 1992 compared to previous 1988-91 data (Reilly et al. 1993). However, port-specific areas of major concern were identified for chilipepper, lingcod, and black rockfish, and to a lesser extent brown, canary, vermilion, yelloweye, widow and greenspotted rockfishes. These areas of concern included steadily declining catch rate, steadily declining mean length, and/or a high percentage of sexually immature fish in the sampled catch. Recent sampling of the commercial hook-and-line fishery in northern and central California indicates that most rockfishes taken by CPFV anglers are also harvested commercially. (105pp.

RISK RESEARCH AND PUBLIC OUTREACH: A TALE OF TWO CULTURES?

Agricultural economists have been challenged in recent years, by voices inside and outside the profession, to evaluate the integrity of the operational bridge between research and extension activities in the land grant system. This essay investigates links between the work of risk researchers and outreach programs. Survey results indicate that (a) a significant number of risk researchers are involved in extension activities; (b) extension economists are less frequently involved in risk research than their colleagues with no extension appointment; (c) full-time extension economists use less sophisticated risk tools in their outreach efforts than used in their research; and (d) all respondents, regardless of appointment, see a need for more applied risk analysis. Major challenges include a lack of financial support to close the data gap and to conduct relevant applied analysis present major communication challenges.Teaching/Communication/Extension/Profession,

Testing the impact of diagenesis on the delta O-18 and delta C-13 of benthic foraminiferal calcite from a sediment burial depth transect in the equatorial Pacific

Stable oxygen and carbon isotope (δ18O and δ13C) values measured in foraminiferal calcite are one of the primary tools used in paleoceanography. Diagenetic recrystallisation of foraminiferal calcite can act to reset primary isotopic values but its effects are typically poorly quantified. Here we test the impact of early stage diagenesis on stable isotope records generated from a suite of drill sites in the equatorial Pacific Ocean recovered during Ocean Drilling Program (ODP) Leg 199 and Integrated Ocean Drilling Program (IODP) Expedition 320. Our selected sites form paleowater- and burial-depth transects, with excellent stratigraphic control allowing us to confidently correlate our records. We observe large inter-site differences in the preservation state of benthic foraminiferal calcite, implying very different recrystallisation histories, but negligible inter-site offsets in benthic δ18O and δ13C values. We infer that diagenetic alteration of benthic foraminiferal calcite (in sedimentary oozes) must predominantly occur at shallow burial depths (<100 m) where offsets in both the temperature and isotopic composition of waters in which the foraminifera calcified and pore-waters in which diagenesis occurs are small. Our results suggest that even extensive recrystallisation of benthic foraminiferal calcite results in minimal shifts from primary δ18O and δ13C values. This finding supports the long-held suspicion that diagenetic alteration of foraminiferal calcite is less problematic in benthic than in planktic foraminifera and that in deep–sea sediments routinely employed for palaeoceanographic studies benthic foraminifera are robust recorders of stable isotope values in the fossil record

Groundwater Conservation Policy in Agriculture

Transboundary water conflicts between urban and rural populations often center on water use in the agricultural sector. Public officials may select a water conservation policy as the primary tool for reducing agricultural water use with the goal to improve water availability to urban areas and future generations. The Groundwater Management Act of 1980 (GMA) in Arizona was designed, in part, to induce water conservation in irrigated agriculture to sustain economic growth in an arid climate. Our mixed-method evaluation design merges qualitative, interview-based information with an estimated water demand function using panel data. We find that the GMA began with a flawed design and evolved through political circumstances into a ineffective water conservation tool. We explain nearly all water use in Arizona's agricultural sector from 1984-2002 using prices and weather data. We found no statistical evidence that the management plans of the GMA directly contributed to reduced water demand in Arizona's agricultural sector over the study period.Impact assessment, public policy, irrigation, water conservation, Resource /Energy Economics and Policy,

Measurement Issues in Assessing Farm Profitability through Cash Tax Returns

It is widely accepted that net farm income reported on an accrual-adjusted income statement is a more appropriate profitability measure than net farm income reported on Schedule F of the federal tax return, which is prepared using cash basis accounting. However, a common practice among agricultural lenders is to use Schedule F net farm income, which uses the cash basis of accounting, as a proxy for accrual-adjusted net farm income. A study of 1,045 individual Illinois farms’ records from 2002 through 2006 found the median absolute annual percentage difference between a three-year average cash and a three-year average accrual-adjusted net farm incomes is 57 percent for farms of stable size; 43 percent for farms with annual gross revenue increasing at rates of less than 5 percent, 50 percent at rates of 5-10 percent, and 58 percent at rates over 10 percent; and 61 percent for farms with a debt-to-asset ratio greater than 40 percent.Agricultural Finance,

Exploring Fiction Writer’s Approaches to Plot Outlining During the Planning Stage of the Writing Process

This thesis is about one person’s discovery and growth as a writer of creative fiction that spans decades. It specifically explores and analyzes how professional authors approach plot outlining during the planning stages of the writing process. Some professional authors prepare plot outlines prior to writing their first draft, while others do not. Over the course of the author’s writing life, experimenting with both methods has been instructive to the development of a personal approach to plot outlining. The Artist statement provides background on the author. Next, the Critical Paper examines and analyzes plot outlining and plot structure. Plot structure and plot types are detailed, followed by a comparative analysis of the plot structure of the novels of three contemporary authors. Finally, the Creative Manuscript demonstrates the author’s attempt at effective story structure in the opening chapters of a novel-length work, A Dex Wing Mess

Spatial Consistency and Contextual Cues for Incidental Learning in Browser Design

This paper introduces the Backward Highlighting technique for mitigating an identified flaw in directional column-faceted browsers like iTunes. Further, the technique significantly enhances the information that can be learned from the columns and encourages further interaction with facet items that were previously restricted from use. After giving a detailed overview of faceted browsing approaches, the Backward Highlighting technique is described along with possible implementations. Two of these possible implementations are compared to a control condition to statistically prove the value of Backward Highlighting. The analysis produces design recommendations for implementing the Backward Highlighting technique within faceted browsers that choose the directional column approach. The paper concludes with future work on how to further improve on the statistically proven advantages provided by the Backward Highlighting technique