Deciphering 3'ss selection in the yeast genome reveals an RNA thermosensor that mediates alternative splicing

Poor understanding of the spliceosomal mechanisms to select intronic 3' ends (3'ss) is a major obstacle to deciphering eukaryotic genomes. Here, we discern the rules for global 3'ss selection in yeast. We show that, in contrast to the uniformity of yeast splicing, the spliceosome uses all available 3'ss within a distance window from the intronic branch site (BS), and that in 70% of all possible 3'ss this is likely to be mediated by pre-mRNA structures. Our results reveal that one of these RNA folds acts as an RNA thermosensor, modulating alternative splicing in response to heat shock by controlling alternate 3'ss availability. Thus, our data point to a deeper role for the pre-mRNA in the control of its own fate, and to a simple mechanism for some alternative splicing.

African signatures of recent positive selection in human FOXI1

Background: The human FOXI1 gene codes for a transcription factor involved in the physiology of the inner ear, testis, and kidney. Using three interspecies comparisons, it has been suggested that this may be a gene underhuman-specific selection. We sought to confirm this finding by using an extended set of orthologous sequences.Additionally, we explored for signals of natural selection within humans by sequencing the gene in 20 Europeans,20 East Asians and 20 Yorubas and by analysing SNP variation in a 2 Mb region centered on FOXI1 in 39worldwide human populations from the HGDP-CEPH diversity panel.Results: The genome sequences recently available from other primate and non-primate species showed that FOXI1divergence patterns are compatible with neutral evolution. Sequence-based neutrality tests were not significant inEuropeans, East Asians or Yorubas. However, the Long Range Haplotype (LRH) test, as well as the iHS and XP-Rsbstatistics revealed significantly extended tracks of homozygosity around FOXI1 in Africa, suggesting a recentepisode of positive selection acting on this gene. A functionally relevant SNP, as well as several SNPs either on theputatively selected core haplotypes or with significant iHS or XP-Rsb values, displayed allele frequencies stronglycorrelated with the absolute geographical latitude of the populations sampled.Conclusions: We present evidence for recent positive selection in the FOXI1 gene region in Africa. Climate mightbe related to this recent adaptive event in humans. Of the multiple functions of FOXI1, its role in kidney-mediatedwater-electrolyte homeostasis is the most obvious candidate for explaining a climate-related adaptation.

Protocol of the COSMIN study: consensus-based standards for the selection of health measurement instruments

Background: Choosing an adequate measurement instrument depends on the proposed use of the instrument, the concept to be measured, the measurement properties (e.g. internal consistency, reproducibility, content and construct validity, responsiveness, and interpretability), the requirements, the burden for subjects, and costs of the available instruments. As far as measurement properties are concerned, there are no sufficiently specific standards for the evaluation of measurement properties of instruments to measure health status, and also no explicit criteria for what constitutes good measurement properties. In this paper we describe the protocol for the COSMIN study, the objective of which is to develop a checklist that contains COnsensus-based Standards for the selection of health Measurement INstruments, including explicit criteria for satisfying these standards. We will focus on evaluative health related patient-reported outcomes (HR-PROs), i.e. patient-reported health measurement instruments used in a longitudinal design as an outcome measure, excluding health care related PROs, such as satisfaction with care or adherence. The COSMIN standards will be made available in the form of an easily applicable checklist.Method: An international Delphi study will be performed to reach consensus on which and how measurement properties should be assessed, and on criteria for good measurement properties. Two sources of input will be used for the Delphi study: (1) a systematic review of properties, standards and criteria of measurement properties found in systematic reviews of measurement instruments, and (2) an additional literature search of methodological articles presenting a comprehensive checklist of standards and criteria. The Delphi study will consist of four (written) Delphi rounds, with approximately 30 expert panel members with different backgrounds in clinical medicine, biostatistics, psychology, and epidemiology. The final checklist will subsequently be field-tested by assessing the inter-rater reproducibility of the checklist.Discussion: Since the study will mainly be anonymous, problems that are commonly encountered in face-to-face group meetings, such as the dominance of certain persons in the communication process, will be avoided. By performing a Delphi study and involving many experts, the likelihood that the checklist will have sufficient credibility to be accepted and implemented will increase.

F-1 Food Assistance Program State Summary, May 2005

The Food Assistance Monthly Participation Report is a monthly summary of Food Assistance program participation, Statewide and for each Iowa county. Breakouts are reported for participants also in the FIP program, those only receiving Food Assistance, and those that are receiving economic assistance under other programs (primarily Medicaid). This report may also be known as the F-1 Report.

F-1 Food Assistance Program State Summary, June 2005

The Food Assistance Monthly Participation Report is a monthly summary of Food Assistance program participation, Statewide and for each Iowa county. Breakouts are reported for participants also in the FIP program, those only receiving Food Assistance, and those that are receiving economic assistance under other programs (primarily Medicaid). This report may also be known as the F-1 Report.

A-8a Summary of Food Stamp Errors Active and Negative Cases, April-September 2004

A-8a Summary of Food Stamp Errors Active and Negative Cases, Apr. 2004 - Sept. 2004

A-8a Summary of Food Stamp Errors Active and Negative Cases, October 2004-March 2005

A-8a Summary of Food Stamp Errors Active and Negative Cases, Oct. 2004 - Mar. 2005

F-1 Food Assistance Program State Summary, July 2005

The Food Assistance Monthly Participation Report is a monthly summary of Food Assistance program participation, Statewide and for each Iowa county. Breakouts are reported for participants also in the FIP program, those only receiving Food Assistance, and those that are receiving economic assistance under other programs (primarily Medicaid). This report may also be known as the F-1 Report.

Rice Consumption in the United States: New Evidence from Food Consumption Surveys, July 2005

Evidence from recent U.S. food consumption surveys provides new information on the distribution of rice consumption, the characteristics of rice consumers, and the diets of people who consume rice. Recently available data from nationally representative surveys of food consumed by individuals in the United States allowed comparison of consumption today (2001-02) with consumption in the mid-1990s. Data come from the Continuing Survey of Food Intakes by Individuals (1994-96) and the National Health and Nutrition Examination Survey (2001-02). Rice is consumed by a significant portion of the U.S. adult population. In 2001-02, over 18 percent (18.2 percent) of adults reported eating at least half a serving of white or brown rice in one day of observed intake. This share was slightly higher than that of 1994-96 (17.4 percent). Compared with others, individuals who consumed at least half a serving of white or brown rice in the observed day of intake consumed a smaller share of calories per day from fat and saturated fat; less discretionary fat or added sugar; and more fiber, dietary folate, fruit, vegetables, and enriched grains. Consumers eating rice were more likely to eat a diet that included choices of foods consistent with the 2005 U.S. Dietary Guidelines.

Dairy Food Consumption, Production, and Policy in Japan, August 2005

We explore and investigate Japanese dairy markets. We first provide an overview of consumer demand and how it evolved after World War II. Using historical data and econometric estimates of Japanese dairy demand, we identify economic, cultural, and demographic forces that have been shaping consumption patterns. Then we summarize the characteristics of Japanese milk production and dairy processing and policies affecting them. We next describe the import regime and trade flows in dairy products. The analysis of the regulatory system of the dairy sector shows how its incentive structure affects the long-term prospects of various segments of the industry. The paper concludes with policy recommendations of how to reform the Japanese dairy sector.

F-1 Food Assistance Program State Summary, August 2005

The Food Assistance Monthly Participation Report is a monthly summary of Food Assistance program participation, Statewide and for each Iowa county. Breakouts are reported for participants also in the FIP program, those only receiving Food Assistance, and those that are receiving economic assistance under other programs (primarily Medicaid). This report may also be known as the F-1 Report.

Edge detection by selection of pieces of level lines

We propose an edge detector based on the selection of wellcontrasted pieces of level lines, following the proposal ofDesolneux-Moisan-Morel (DMM) [1]. The DMM edge detectorhas the problem of over-representation, that is, everyedge is detected several times in slightly different positions.In this paper we propose two modifications of the originalDMM edge detector in order to solve this problem. The firstmodification is a post-processing of the output using a generalmethod to select the best representative of a bundle of curves.The second modification is the use of Canny’s edge detectorinstead of the norm of the gradient to build the statistics. Thetwo modifications are independent and can be applied separately.Elementary reasoning and some experiments showthat the best results are obtained when both modifications areapplied together.

Lithuania’s Food Demand During Economic Transition, January 2000

The linear approximate version of the AIDS model is estimated using data from the Lithuanian household budget survey covering the period from July 1992 to December 1994. Price and real expenditure elasticities for twelve food groups were estimated based on the estimated coefficients of the model. Very little or nothing is known about the demand parameters of Lithuania and other former socialist countries, so the results are of intrinsic interest. Estimated expenditure elasticities were positive and statistically significant for all food groups while all own-price elasticities were negative and statistically significant, except for that of eggs which was insignificant. Results suggest that Lithuanian household consumption did respond to price and real income changes during their transition to a market-oriented economy.

Duplication and concerted evolution in a master sex determiner under balancing selection.

The transformer (tra) gene is a key regulator in the signalling hierarchy controlling all aspects of somatic sexual differentiation in Drosophila and other insects. Here, we show that six of the seven sequenced ants have two copies of tra. Surprisingly, the two paralogues are always more similar within species than among species. Comparative sequence analyses indicate that this pattern is owing to the ongoing concerted evolution after an ancestral duplication rather than independent duplications in each of the six species. In particular, there was strong support for inter-locus recombination between the paralogues of the ant Atta cephalotes. In the five species where the location of paralogues is known, they are adjacent to each other in four cases and separated by only few genes in the fifth case. Because there have been extensive genomic rearrangements in these lineages, this suggests selection acting to conserve their synteny. In three species, we also find a signature of positive selection in one of the paralogues. In three bee species where information is available, the tra gene is also duplicated, the copies are adjacent and in at least one species there was recombination between paralogues. These results suggest that concerted evolution plays an adaptive role in the evolution of this gene family.

F-1 Food Assistance Program State Summary, September 2005

The Food Assistance Monthly Participation Report is a monthly summary of Food Assistance program participation, Statewide and for each Iowa county. Breakouts are reported for participants also in the FIP program, those only receiving Food Assistance, and those that are receiving economic assistance under other programs (primarily Medicaid). This report may also be known as the F-1 Report.