Improving Gene-finding in Chlamydomonas reinhardtii:GreenGenie2

<p>Abstract</p> <p>Background</p> <p>The availability of whole-genome sequences allows for the identification of the entire set of protein coding genes as well as their regulatory regions. This can be accomplished using multiple complementary methods that include ESTs, homology searches and <it>ab initio </it>gene predictions. Previously, the Genie gene-finding algorithm was trained on a small set of <it>Chlamydomonas </it>genes and shown to improve the accuracy of gene prediction in this species compared to other available programs. To improve <it>ab initio </it>gene finding in <it>Chlamydomonas</it>, we assemble a new training set consisting of over 2,300 cDNAs by assembling over 167,000 <it>Chlamydomonas </it>EST entries in GenBank using the EST assembly tool PASA.</p> <p>Results</p> <p>The prediction accuracy of our cDNA-trained gene-finder, GreenGenie2, attains 83% sensitivity and 83% specificity for exons on short-sequence predictions. We predict about 12,000 genes in the version <it>v3 Chlamydomonas </it>genome assembly, most of which (78%) are either identical to or significantly overlap the published catalog of <it>Chlamydomonas </it>genes <abbrgrp><abbr bid="B1">1</abbr></abbrgrp>. 22% of the published catalog is absent from the GreenGenie2 predictions; there is also a fraction (23%) of GreenGenie2 predictions that are absent from the published gene catalog. Randomly chosen gene models were tested by RT-PCR and most support the GreenGenie2 predictions.</p> <p>Conclusion</p> <p>These data suggest that training with EST assemblies is highly effective and that GreenGenie2 is a valuable, complementary tool for predicting genes in <it>Chlamydomonas reinhardtii</it>.</p

The Grizzly, April 24, 1987

Professor: One of Eighty Arrested for Protest • Forum Series Ends • Spring Weekend Lacks Enthusiasm • Admissions Expands to New Areas • Letters: Room Selection Process Attacked; Another Attack; Apology; And a Different Response • Students Represent U.C. in D.C. at Center • Chapter Scholars Announced • Notes: Singing Instructions Begin; Student Musician Presents Recital • Final Exam Schedule • Bears Offensive Team Sweeps Haverford Double Header • Crowded House Instruments Variety • Brown Urges Students to Pump on For Fourth Annual Lift-A-Thon • Wood and Lucky Number 13 Gives Runners Record • Tennis Courts Wins • Lady LAX Team Rolling Towards NCAA\u27s • Netters Frustrated in Attempt to Reach End of Season .500 • Athlete of the Week: John Woodhttps://digitalcommons.ursinus.edu/grizzlynews/1188/thumbnail.jp

The Grizzly, April 10, 1987

Pfahler Hall Flooded • L.C.B. Visits a Second Time • Our Town Debuts • Letters: Director of Security at Sheraton Responds to Student Attack on Lorelei; Brothers of AXE Commended; Grizzly Dogged • Skunked Again • Students to Participate in Model UN Conference • Salamanca to Relate Experiences on Terrorism • Bard Graces Ursinus • Notes: UC / St. Joseph\u27s Host MBA Summer Session; Myrin Holds Semi-Annual Book Sale; New Resident Assistants Announced • Athlete of the Week: Kim Wentzel • Santangelo, O\u27Malley Jump Lady Bears to 6-0 Start • Women\u27s Tennis Served Tough Losses • Track\u27s Record: Record Breaking • Ursinus\u27 Champion Lacrosse Team: Vying for Fourth National Title • Opposition Unfavorable to Bears • Golf Team Drives Record to 8-0 • Softball Assumes First Place Position • Room Selection to Start • The Joshua Tree Rates an A • Young Democrats: Exhibiting New Challenges for the Future • Advanced TV Class Produces Ursinus Magazine For Cable Network • Arbor Day Trees Grow Money • Bear Facts: Ursinus Mascot Bearly Knownhttps://digitalcommons.ursinus.edu/grizzlynews/1187/thumbnail.jp

The Grizzly, May 1, 1987

Will Ursinus Make the Grade? • Commuters Recognized • Student Apathy a Farce • Beatles Now Available on Disc • Dougy is King to Sig Rho • Notes: Summer Tennis Strategies Offered; Continuing Ed. Becomes Assertive; Physical Education Day: May 4th; Band and Jazz Ensemble to Perform • Lacrosse Shoots for 4th Title; Bingaman Breaks Another Record • MAC\u27s Return to Ursinus; Bears Look to Usurp Crown • Golf Ties Record at 15-1: Klee, Ignatowicz Lead Bears to MAC Fifth • Trout Tourney Results • The Men Looking For Glory • Baseball Season Ends on Down Note • Kulp Driven to Excellence • Softball Denied Playoffs • Women Netters .500 • Dolman Leaves with Warm Feelings • Renovations at Myrin • Zucker Retires to Further Musical Interests • Multi-talented Symons Ends Forty Year Career at Ursinus • Page Closes the Book at Ursinushttps://digitalcommons.ursinus.edu/grizzlynews/1189/thumbnail.jp

An Analysis of the Systemic Risks Posed by Fannie Mae and Freddie Mac and an Evaluation of the Policy Options for Reducing those Risks

Fannie Mae and Freddie Mac are government-sponsored enterprises that are central players in U.S. secondary mortgage markets. Over the past decade, these institutions have amassed enormous mortgage- and non-mortgage-oriented investment portfolios that pose significant interest-rate risks to the companies and a systemic risk to the financial system. This paper describes the nature of these risks and systemic concerns and then evaluates several policy options for reducing the institutions’ investment portfolios. We conclude that limits on portfolio size (assets or liabilities) would be the most desirable approach to mitigating the systemic risk posed by Fannie Mae and Freddie Mac

Consequences of twenty-first-century policy for multi-millennial climate and sea-level change

Most of the policy debate surrounding the actions needed to mitigate and adapt to anthropogenic climate change has been framed by observations of the past 150 years as well as climate and sea-level projections for the twenty-first century. The focus on this 250-year window, however, obscures some of the most profound problems associated with climate change. Here, we argue that the twentieth and twenty-first centuries, a period during which the overwhelming majority of human-caused carbon emissions are likely to occur, need to be placed into a long-term context that includes the past 20 millennia, when the last Ice Age ended and human civilization developed, and the next ten millennia, over which time the projected impacts of anthropogenic climate change will grow and persist. This long-term perspective illustrates that policy decisions made in the next few years to decades will have profound impacts on global climate, ecosystems and human societies — not just for this century, but for the next ten millennia and beyond.This is the publisher’s final pdf. The published article is copyrighted by Nature Publishing Group and can be found at: http://www.nature.com/nclimate/index.htm

The James Webb Space Telescope Mission

Twenty-six years ago a small committee report, building on earlier studies, expounded a compelling and poetic vision for the future of astronomy, calling for an infrared-optimized space telescope with an aperture of at least $4m$. With the support of their governments in the US, Europe, and Canada, 20,000 people realized that vision as the $6.5m$ James Webb Space Telescope. A generation of astronomers will celebrate their accomplishments for the life of the mission, potentially as long as 20 years, and beyond. This report and the scientific discoveries that follow are extended thank-you notes to the 20,000 team members. The telescope is working perfectly, with much better image quality than expected. In this and accompanying papers, we give a brief history, describe the observatory, outline its objectives and current observing program, and discuss the inventions and people who made it possible. We cite detailed reports on the design and the measured performance on orbit.Comment: Accepted by PASP for the special issue on The James Webb Space Telescope Overview, 29 pages, 4 figure

Interrelated performance measures, interactive effort, and optimal incentives

All in-text references underlined in blue are linked to publications on ResearchGate, letting you access and read them immediately

Effectiveness of vergence/accommodative therapy for accommodative dysfunction in children with convergence insufficiency

To determine the effectiveness of office-based vergence/accommodative therapy for improving accommodative amplitude and accommodative facility in children with symptomatic convergence insufficiency and accommodative dysfunction. We report changes in accommodative function following therapy among participants in the Convergence Insufficiency Treatment Trial - Attention and Reading Trial with decreased accommodative amplitude (115 participants in vergence/accommodative therapy; 65 in placebo therapy) or decreased accommodative facility (71 participants in vergence/accommodative therapy; 37 in placebo therapy) at baseline. The primary analysis compared mean change in amplitude and facility between the vergence/accommodative and placebo therapy groups using analyses of variance models after 4, 8, 12 and 16 weeks of treatment. The proportions of participants with normal amplitude and facility at each time point were calculated. The average rate of change in amplitude and facility from baseline to week 4, and from weeks 4 to 16, were determined in the vergence/accommodative therapy group. From baseline to 16 weeks, the mean improvement in amplitude was 8.6 dioptres (D) and 5.2 D in the vergence/accommodative and placebo therapy groups, respectively (mean difference = 3.5 D, 95% confidence interval (CI): 1.5 to 5.5 D; p = 0.01). The mean improvement in facility was 13.5 cycles per minute (cpm) and 7.6 cpm in the vergence/accommodative and placebo therapy groups, respectively (mean difference = 5.8 cpm, 95% CI: 3.8 to 7.9 cpm; p < 0.0001). Significantly greater proportions of participants treated with vergence/accommodative therapy achieved a normal amplitude (69% vs. 32%, difference = 37%, 95% CI: 22 to 51%; p < 0.0001) and facility (85% vs. 49%, difference = 36%, 95% CI: 18 to 55%; p < 0.0001) than those who received placebo therapy. In the vergence/accommodative therapy group, amplitude increased at an average rate of 1.5 D per week during the first 4 weeks (p < 0.0001), then slowed to 0.2 D per week (p = 0.002) from weeks 4 to 16. Similarly, facility increased at an average rate of 1.5 cpm per week during the first 4 weeks (p < 0.0001), then slowed to 0.6 cpm per week from weeks 4 to 16 (p < 0.0001). Office-based vergence/accommodative therapy is effective for improving accommodative function in children with symptomatic convergence insufficiency and coexisting accommodative dysfunction