The GENCODE pseudogene resource.

BACKGROUND: Pseudogenes have long been considered as nonfunctional genomic sequences. However, recent evidence suggests that many of them might have some form of biological activity, and the possibility of functionality has increased interest in their accurate annotation and integration with functional genomics data. RESULTS: As part of the GENCODE annotation of the human genome, we present the first genome-wide pseudogene assignment for protein-coding genes, based on both large-scale manual annotation and in silico pipelines. A key aspect of this coupled approach is that it allows us to identify pseudogenes in an unbiased fashion as well as untangle complex events through manual evaluation. We integrate the pseudogene annotations with the extensive ENCODE functional genomics information. In particular, we determine the expression level, transcription-factor and RNA polymerase II binding, and chromatin marks associated with each pseudogene. Based on their distribution, we develop simple statistical models for each type of activity, which we validate with large-scale RT-PCR-Seq experiments. Finally, we compare our pseudogenes with conservation and variation data from primate alignments and the 1000 Genomes project, producing lists of pseudogenes potentially under selection. CONCLUSIONS: At one extreme, some pseudogenes possess conventional characteristics of functionality; these may represent genes that have recently died. On the other hand, we find interesting patterns of partial activity, which may suggest that dead genes are being resurrected as functioning non-coding RNAs. The activity data of each pseudogene are stored in an associated resource, psiDR, which will be useful for the initial identification of potentially functional pseudogenes.

Nutrient allocation, accumulation and above-ground biomass in grey alder and hybrid alder plantations

Abstract

Growth and biomass allocation of the C4 grasses Brachiaria brizantha and B. humidicola under shade

The growth and biomass allocation responses of the tropical forage grasses Brachiaria brizantha cv. Marandu and B. humidicola were compared for plants grown outdoors, in pots, in full sunlight and those shaded to 30% of full sunlight over a 30day period. The objective was to evaluate the acclimation capacity of these species to low light. Both species were able to quickly develop phenotypic adjustments in response to low light. Specific leaf area and leaf area ratio were higher for low-light plants during the entire experimental period. Low-light plants allocated significantly less biomass to root and more to leaf tissue than high-light plants. However, the biomass allocation pattern to culms was different for the two species under low light: it increased in B. brizantha, but decreased in B. humidicola, probably as a reflection of the growth habits of these species. Relative growth rate and tillering were higher in high-light plants. Leaf elongation rate was significantly increased on both species under low light; however, the difference between treatments was higher in B. brizantha. These results are discussed in relation to the pasture management implications.

An Optimum Allocation Approach to Closing or Relocating Highway Maintenance Garages in Iowa, 1981

Highway maintenance engineers and administrators are often confronted with a number of problems related to highway maintenance work programs. One of these problems is concerned with determining the optimum number and locations of highway maintenance garages in a given area. Serious decline in highway revenues and a high inflation rate have made it necessary to examine existing maintenance practices and to allocate reduced financial resources more effectively and efficiently. Searching for and providing of reasonable solutions to these problems is the focus of this research project. The methodology used is to identify and modify for use (if necessary) those models which have already been developed. Models which could give optimum number and locations of highway maintenance garages were found to be too theoretical and/or practically infeasible. Consequently, research focus was shifted from these models to other models that could compare alternatives and select the best among these alternatives. Three such models -- the Alabama model, California model, and Louisiana model, were identified and studied.

Effects of group size and space allocation on physiological, behavioural and production-related welfare parameters in farmed silver fox cubs

Selostus: Ryhmäkoon ja käytössä olevan tilan vaikutus tarhattujen hopeakettupentujen hyvinvointiin

Iowa Department of Naturals Resource Performance Report, FY 2013-2014, January 2014

This report provides insight on accomplishments we have achieved in Fiscal Year 2015 as well as some challenges we face in the not so distant future. The DNR, in partnership with the Iowa Department of Agriculture and Land Stewardship and Iowa State University,

An application of capital allocation principles to operational risk

The cost of operational risk refers to the capital needed to a fford the loss generated by ordinary activities of a firm. In this work we demonstrate how allocation principles can be used to the subdivision of the aggregate capital so that the firm can distribute this cost across its various constituents that generate operational risk. Several capital allocation principles are revised. Proportional allocation allows to calculate a relative risk premium to be charged to each unit. An example of fraud risk in the banking sector is presented and some correlation scenarios between business lines are compared. Keywords: solvency, quantile, value at risk, copulas

Allocation of above-ground growth in Pinus sylvestris - impacts of tree size and competition

Abstract

ViralZone: recent updates to the virus knowledge resource.

ViralZone (http://viralzone.expasy.org) is a knowledge repository that allows users to learn about viruses including their virion structure, replication cycle and host-virus interactions. The information is divided into viral fact sheets that describe virion shape, molecular biology and epidemiology for each viral genus, with links to the corresponding annotated proteomes of UniProtKB. Each viral genus page contains detailed illustrations, text and PubMed references. This new update provides a linked view of viral molecular biology through 133 new viral ontology pages that describe common steps of viral replication cycles shared by several viral genera. This viral cell-cycle ontology is also represented in UniProtKB in the form of annotated keywords. In this way, users can navigate from the description of a replication-cycle event, to the viral genus concerned, and the associated UniProtKB protein records.

Iowa Department of Naturals Resource Agency Performance Plan, FY2015, July 1, 2014

This report provides insight on accomplishments the department of Natural Resources have achieved in Fiscal Year 2015 as well as some challenges face in the not so distant future.

Iowa's People: a resource for extension educators, June 1989

Statistics about people and their families interest community planners, social scientists, Extension educators, and others because the family is the fundamental social institution in our society. The purpose of this publication is to bring together in one reference many statistics about people in Iowa counties that have been published separately elsewhere. Most of the data presented are limited to only one year. This cross-sectional view is similar to a photograph that shows only one point in time. At an earlier or later time it might appear differently. Although the statistics reported in the various tables and figures represent different years, the data presented were the most recent available at the time this publication was prepared.