DNA Motif Match Statistics Without Poisson Approximation

Transcription factors (TFs) play a crucial role in gene regulation by binding to specific regulatory sequences. The sequence motifs recognized by a TF can be described in terms of position frequency matrices. Searching for motif matches with a given position frequency matrix is achieved by employing a predefined score cutoff and subsequently counting the number of matches above this cutoff. In this article, we approximate the distribution of the number of motif matches based on a novel dynamic programming approach, which accounts for higher order sequence background (e.g., as is characteristic for CpG islands) and overlapping motif matches on both DNA strands. A comparison with our previously published compound Poisson approximation and a binomial approximation demonstrates that in particular for relaxed score thresholds, the dynamic programming approach yields more accurate results

Winona Daily News

https://openriver.winona.edu/winonadailynews/2241/thumbnail.jp

Pattern Recognition

A wealth of advanced pattern recognition algorithms are emerging from the interdiscipline between technologies of effective visual features and the human-brain cognition process. Effective visual features are made possible through the rapid developments in appropriate sensor equipments, novel filter designs, and viable information processing architectures. While the understanding of human-brain cognition process broadens the way in which the computer can perform pattern recognition tasks. The present book is intended to collect representative researches around the globe focusing on low-level vision, filter design, features and image descriptors, data mining and analysis, and biologically inspired algorithms. The 27 chapters coved in this book disclose recent advances and new ideas in promoting the techniques, technology and applications of pattern recognition

Farmstead Magazine, Harvest 1981

https://digitalmaine.com/farmstead_magazine/1046/thumbnail.jp

Farmstead Magazine, Harvest 1981

https://digitalmaine.com/farmstead_magazine/1046/thumbnail.jp

Development and application of electron microscopy methods for endocytic-secretory pathway studies in cells

Electron microscopy (EM) and tomography provides the most detailed view of the cellular ultrastructure and can be further extended to the structural level using cryogenic electron tomography. Fluorescent microscopy (FM) is used to complement this data with molecular identity information in a wide range of correlative microscopy techniques. In this thesis I present my work on the development of the correlative microscopy methods as well as the application of new and established electron microscopy methods to the study of the endocytic and secretory pathways. I developed a sample parallelization approach based on the fluorescent barcoding of budding yeast cells that allows high-throughput screening of yeast mutants using EM. Cells from different strains or under different conditions are grown in parallel and then subjected to combinatorial labeling with fluorescent dyes. Labeled cells are mixed together to generate a single sample which is subjected to high-pressure freezing, freeze-substitution and sectioning. The sections are imaged with FM and EM. FM data is used to determine the fluorescent barcode of each cell and thus its strain identity or experimental conditions, and high-resolution EM data can be collected in parallel for each of the strains or conditions. The total time spent on embedding and sectioning can be reduced up to 30 times using the developed protocol. I demonstrate the utility of the method by analyzing the variation of total multivesicular body volume (MVB) in different yeast strains. As a part of the collaborative project investigating the role of the ATPase Vps4 in the formation of MVBs, I performed correlative FM and electron tomography of MVBs containing Vps4. It showed that MVBs correlating with the Vps4 signal usually form clusters of more than one organelle and that the Vps4 signal correlates with MVBs actively forming intraluminal vesicles. Finally, I used subtomogram averaging to determine the COPI coat structure in situ, within its native cellular environment. I analyzed a tomographic dataset of cryo-lamella prepared by collaborators using focused ion beam milling of vitrified Chlamydomonas reinhardtii cells. I determined the COPI coat structure de novo and analyzed its variability during uncoating and within the Golgi stack. The COPI coat preserved its structure and stoichiometry during uncoating and in different Golgi regions. However the density of bound dilysine cargo and membrane thickness varied along the stack. In this thesis I have applied different EM methods to investigate morphological and structural aspects of the endocytic-secretory pathway. In the future such an integrative EM approach, ranging from functional genetic screens to structure determination, can be used to address multiple questions in cell biology

Missing Letters: Seven stories and one novella

My MFA thesis, entitled MISSING LETTERS, consists of seven short stories and one novella. These pieces are arranged to reflect a variety of tone and style; The first story, Tale of the Ill Ook Ook, is strictly comedic and serves as a parody of adult book stores. The emphasis is on humor rather than eroticism; The second story is Trouble on the Farm, which is intense in its treatment of a troubled runaway teen with murder and vengeance on his mind; Story number three, The Romans, is a children\u27s story, featuring Scotty, the protagonist who headlines my first published novel, SCOTTY AND THE GYPSY BANDIT. A sense of morality motors through this and story number seven, The Lemonade Stand. . Both are constructed in a sparse, lean style that reflects the simplistic yet morally compromised world of childhood; Wanda Waits is a dark, tightly structured tale concerning a hit man who would prefer a different line of work, but the money is too good for him to quit; Joie de Vivre tells the story of a strained father/daughter relationship with a dead mother as its centerpiece; Are We There Yet? is a light-hearted satire of the Book of Exodus, with a considerable amount of wordplay and puns, featuring a Las Vegas setting; The operative theme of my novella, Odd Bodkins, is the dissipation of a marriage brought on by a third party. It strives for a more literary-like style

Using MapReduce Streaming for Distributed Life Simulation on the Cloud

Distributed software simulations are indispensable in the study of large-scale life models but often require the use of technically complex lower-level distributed computing frameworks, such as MPI. We propose to overcome the complexity challenge by applying the emerging MapReduce (MR) model to distributed life simulations and by running such simulations on the cloud. Technically, we design optimized MR streaming algorithms for discrete and continuous versions of Conway’s life according to a general MR streaming pattern. We chose life because it is simple enough as a testbed for MR’s applicability to a-life simulations and general enough to make our results applicable to various lattice-based a-life models. We implement and empirically evaluate our algorithms’ performance on Amazon’s Elastic MR cloud. Our experiments demonstrate that a single MR optimization technique called strip partitioning can reduce the execution time of continuous life simulations by 64%. To the best of our knowledge, we are the first to propose and evaluate MR streaming algorithms for lattice-based simulations. Our algorithms can serve as prototypes in the development of novel MR simulation algorithms for large-scale lattice-based a-life models.https://digitalcommons.chapman.edu/scs_books/1014/thumbnail.jp