Semi-restricted Rock, Paper, Scissors

Consider the following variant of Rock, Paper, Scissors (RPS) played by two players Rei and Norman. The game consists of $3n$ rounds of RPS, with the twist being that Rei (the restricted player) must use each of Rock, Paper, and Scissors exactly $n$ times during the $3n$ rounds, while Norman is allowed to play normally without any restrictions. Answering a question of Spiro, we show that a certain greedy strategy is the unique optimal strategy for Rei in this game, and that Norman's expected score is $\Theta(\sqrt{n})$. Moreover, we study semi-restricted versions of general zero sum games and prove a number of results concerning their optimal strategies and expected scores, which in particular implies our results for semi-restricted RPS.Comment: 21 pages, 5 page appendi

Vision and Learning for Deliberative Monocular Cluttered Flight

Cameras provide a rich source of information while being passive, cheap and lightweight for small and medium Unmanned Aerial Vehicles (UAVs). In this work we present the first implementation of receding horizon control, which is widely used in ground vehicles, with monocular vision as the only sensing mode for autonomous UAV flight in dense clutter. We make it feasible on UAVs via a number of contributions: novel coupling of perception and control via relevant and diverse, multiple interpretations of the scene around the robot, leveraging recent advances in machine learning to showcase anytime budgeted cost-sensitive feature selection, and fast non-linear regression for monocular depth prediction. We empirically demonstrate the efficacy of our novel pipeline via real world experiments of more than 2 kms through dense trees with a quadrotor built from off-the-shelf parts. Moreover our pipeline is designed to combine information from other modalities like stereo and lidar as well if available

Systematic evaluation of the impact of ChIP-seq read designs on genome coverage, peak identification, and allele-specific binding detection

Background: Chromatin immunoprecipitation followed by sequencing (ChIP-seq) experiments revolutionized genome-wide profiling of transcription factors and histone modifications. Although maturing sequencing technologies allow these experiments to be carried out with short (36–50 bps), long (75–100 bps), single-end, or paired-end reads, the impact of these read parameters on the downstream data analysis are not well understood. In this paper, we evaluate the effects of different read parameters on genome sequence alignment, coverage of different classes of genomic features, peak identification, and allele-specific binding detection. Results: We generated 101 bps paired-end ChIP-seq data for many transcription factors from human GM12878 and MCF7 cell lines. Systematic evaluations using in silico variations of these data as well as fully simulated data, revealed complex interplay between the sequencing parameters and analysis tools, and indicated clear advantages of paired-end designs in several aspects such as alignment accuracy, peak resolution, and most notably, allele-specific binding detection. Conclusions: Our work elucidates the effect of design on the downstream analysis and provides insights to investigators in deciding sequencing parameters in ChIP-seq experiments. We present the first systematic evaluation of the impact of ChIP-seq designs on allele-specific binding detection and highlights the power of pair-end designs in such studies

Systematic evaluation of the impact of ChIP-seq read designs on genome coverage, peak identification, and allele-specific binding detection

Background: Chromatin immunoprecipitation followed by sequencing (ChIP-seq) experiments revolutionized genome-wide profiling of transcription factors and histone modifications. Although maturing sequencing technologies allow these experiments to be carried out with short (36–50 bps), long (75–100 bps), single-end, or paired-end reads, the impact of these read parameters on the downstream data analysis are not well understood. In this paper, we evaluate the effects of different read parameters on genome sequence alignment, coverage of different classes of genomic features, peak identification, and allele-specific binding detection. Results: We generated 101 bps paired-end ChIP-seq data for many transcription factors from human GM12878 and MCF7 cell lines. Systematic evaluations using in silico variations of these data as well as fully simulated data, revealed complex interplay between the sequencing parameters and analysis tools, and indicated clear advantages of paired-end designs in several aspects such as alignment accuracy, peak resolution, and most notably, allele-specific binding detection. Conclusions: Our work elucidates the effect of design on the downstream analysis and provides insights to investigators in deciding sequencing parameters in ChIP-seq experiments. We present the first systematic evaluation of the impact of ChIP-seq designs on allele-specific binding detection and highlights the power of pair-end designs in such studies

Clusters of microRNAs emerge by new hairpins in existing transcripts

Genetic linkage may result in the expression of multiple products from a polycistronic transcript, under the control of a single promoter. In animals, protein-coding polycistronic transcripts are rare. However, microRNAs are frequently clustered in the genomes of animals, and these clusters are often transcribed as a single unit. The evolution of microRNA clusters has been the subject of much speculation, and a selective advantage of clusters of functionally related microRNAs is often proposed. However, the origin of microRNA clusters has not been so far explored. Here, we study the evolution of microRNA clusters in Drosophila melanogaster. We observed that the majority of microRNA clusters arose by the de novo formation of new microRNA-like hairpins in existing microRNA transcripts. Some clusters also emerged by tandem duplication of a single microRNA. Comparative genomics show that these clusters are unlikely to split or undergo rearrangements. We did not find any instances of clusters appearing by rearrangement of pre-existing microRNA genes. We propose a model for microRNA cluster evolution in which selection over one of the microRNAs in the cluster interferes with the evolution of the other linked microRNAs. Our analysis suggests that the study of microRNAs and small RNAs must consider linkage associations

The dry season intensity as a key driver of NPP trends

We analyze the impacts of changing dry season length and intensity on vegetation productivity and biomass. Our results show a wetness asymmetry in dry ecosystems, with dry seasons becoming drier and wet seasons becoming wetter, likely caused by climate change. The increasingly intense dry seasons were consistently correlated with a decreasing trend in net primary productivity (NPP) and biomass from different products and could potentially mean a reduction of 10–13% in NPP by 2100. We found that annual NPP in dry ecosystems is particularly sensitive to the intensity of the dry season, whereas an increase in precipitation during the wet season has a smaller effect. We conclude that changes in water availability over the dry season affect vegetation throughout the whole year, driving changes in regional NPP. Moreover, these results suggest that usage of seasonal water fluxes is necessary to improve our understanding of the link between water availability and the land carbon cycle