TASK DEFINITION: Given a context passage, generate a question from the passage such that its answer is shortest continous span from the passage.
PROBLEM: The blockage of transcription elongation by RNA polymerase II (pol II) at a DNA damage site on the transcribed strand triggers a transcription-coupled DNA repair (TCR), which rapidly removes DNA damage on the transcribed strand of the expressed gene and allows the resumption of transcription. To analyze the effect of UV-induced DNA damage on transcription elongation, an in vitro transcription elongation system using pol II and oligo(dC)-tailed templates containing a cyclobutane pyrimidine dimer (CPD) or 6-4 photoproduct (6-4PP) at a specific site was employed. The results showed that pol II incorporated nucleotides opposite the CPD and 6-4PP and then stalled. Pol II formed a stable ternary complex consisting of pol II, the DNA damage template, and the nascent transcript. Furthermore, atomic force microscopy imaging revealed that pol II stalled at the damaged region. These findings may provide the basis for analysis of the initiation step of TCR.

SOLUTION: Which gene strand is targeted by transcription-coupled repair (TCR)?

PROBLEM: In cancer research, background models for mutation rates have been extensively calibrated in coding regions, leading to the identification of many driver genes, recurrently mutated more than expected. Noncoding regions are also associated with disease; however, background models for them have not been investigated in as much detail. This is partially due to limited noncoding functional annotation. Also, great mutation heterogeneity and potential correlations between neighboring sites give rise to substantial overdispersion in mutation count, resulting in problematic background rate estimation. Here, we address these issues with a new computational framework called LARVA. It integrates variants with a comprehensive set of noncoding functional elements, modeling the mutation counts of the elements with a -binomial distribution to handle overdispersion. LARVA, moreover, uses regional genomic features such as replication timing to better estimate local mutation rates and mutational hotspots. We demonstrate LARVA's effectiveness on 760 whole-genome tumor sequences, showing that it identifies well-known noncoding drivers, such as mutations in the TERT promoter. Furthermore, LARVA highlights several novel highly mutated regulatory sites that could potentially be noncoding drivers. We make LARVA available as a software tool and release our highly mutated annotations as an online resource (larva.gersteinlab.org).

SOLUTION: Which tool is used for the identification of recurrent variants in noncoding regions?

PROBLEM: The movie opens with the Barden Bellas about to perform at the ICCA championships. One of them, Chloe (Brittany Snow) is running late to the start of the performance. When she arrives she is reprimanded by the older Bellas. As they are about to perform, Aubrey (Anna Camp) tries to assure them she'll do a good job, but is shot down. The group sings 'The Sign'.. and all is going well, until the very end when Aubrey has a solo, and projectile vomits all over the stage and front rows of the audience.Cut to the start of a new year at Barden University, and freshman Beca (Anna Kendrick) is arriving by taxi. While she is receiving directions and her Rape Whistle, a car passes her by, and another student, Jesse (Skylar Austin) is singing along to the radio, and catches her attention.Beca finds her new dorm room, and meets her roommate Kimmy-Jin, who is hostile and unfriendly. Beca's dad, a professor at Barden then arrives, and asks her how she got there. It is revealed that Beca's parents have split up as she refers to her dad's new wife as her 'step monster', and seems very reluctant to be attending College. Beca's dad tries to encourage her to enjoy it, but Beca escapes to the Activities fair.In another dorm room, Jesse is meeting his roommate Benji (Ben Platt), who is into Star Wars and magic.At the Activities fair, we are introduced to the Trebles - one of the Campus singing groups, all male, who are talented and have a high opinion of themselves, especially Bumper (Adam Devine) the lead singer. Jesse and Benji approach the Trebles, as Benji is desperate to join, but Bumper is not impressed with his enthusiasm.Across the campus, the Bellas are now down to just 2 members - Aubrey and Chloe, who are trying to recruit new ones. Due to their disastrous performance at the last Championships, they are not having much luck, and are even ridiculed by 'Baloney Barb' who has tried out for them previously. They are then approached by Fat Amy (Rebel Wilson), an outgoing and quirky student from Tasmania who doesn't hesitate to demonstrate her singing and dancing abilities. They then meet Beca, who quickly rebuffs their offer to audition, saying it is lame, which immediately puts Aubrey offside.Instead of being interested in joining any of the singing groups, Beca has much more of an interest in remixing music on her laptop. She gets a job at the campus radio station, and much to her dismay, so does Jesse.Her dad pays her a visit in her dorm, and gives her an ultimatum - if she makes an effort and joins a group at College , but still doesn't like it by the end of the year, she can quit and follow her true dream of becoming a DJ, and he will help her... but he wants her to really make an effort.As Beca goes into the communal showers singing to herself, Chloe happens to be in the showers as well, and confronts Beca in her shower stall , insisting that she try out for the Bellas. Although Beca is mortified, she sings along with Chloe to 'Titanium'.Finally the auditions are on, and Jesse, Benji and Fat Amy are among the hopefuls trying out, auditioning to 'Since you've been gone'. Beca comes late, and hasn't prepared the audition song, but auditions with 'Cups (miss me when I'm gone)', and Chloe and Jesse are impressed, while Aubrey is unsure. We then see the initiation of the new Bellas including Beca, Fat Amy, Stacie (Alexis Knapp), Cynthia-Rose (Esther Dean) and the very softly spoken Lilly (Hana Mae Lee). They all swear an oath and drink the 'blood of the Bellas who came before them' (wine). Cut to the initiation of the new Trebles.. Jesse has made it, but Benji has not. That night, there is Aca-initiation where all the groups

SOLUTION:
Who provides an impromptu back-up of one of her favorite songs into the "traditional" song?