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Reworking BugSeq-er2 to streamline metagenomics binning using DAS Tool
No full textThe bacterial composition of the gut microbiome is thought to be the root of many health issues in organisms and has become an important topic of investigation in the scientific community. With trillions of microbes across thousands of species present in a single human gut, it is nearly impossible to manually investigate and observe differences without the aid of bioinformatics. Many labs create their own pipelines for data analysis that suit their individual needs, often utilizing open-source programs provided by bioinformaticians all over the world. The Clayton Lab has created a pipeline known as BugSeq-er2 that can process next generation sequencing data generated from biological samples and return information regarding bacterial composition. Throughout the pipeline, sequence reads are analyzed before they are organized into groups known as bins, which provide the lab with data on what bacterial genomes remain in the gut microbiome after each run of the experiment. The binning section of the prototype pipeline had higher than expected runtime for the pipeline to be used efficiently in the lab and did not adopt an effective file management schema. The prototype pipeline took \u3e12 hours to run and the final data files were ineffectively organized, making data retrieval inefficient. To fix the output file management, the code needed to be altered to handle N amounts of output files before concatenating (joining) them into a single output file that is easy for the user to retrieve. To do this, we used the workflow management system Snakemake and additional bash scripting to modify the preexisting code by changing the rule structure within the code to meet the previously mentioned goals. By changing the code, we have found and removed redundant file structures, reorganized the binning process of the pipeline, and have significantly reduced the total runtime for the BugSeq-er2 pipeline
The Artist
No full textBeing a confident woman is one thing, but to be empowered and to embrace femineity sometimes can be difficult in today’s world. Due to beauty standards seen on television, magazines, and social media, I know some women and certainly myself feel as though we can never be the ideal women because of these standards. Inspired by a photograph that my wonderful sister took of me during her annual photoshoot that she does to help empower women, I created self-portrait using one of the photographs she took of me for reference. The reason I chose to do this was so that I could have a reminder that I am beautiful in my own skin, and I do not have to live up to society’s standards to feel beautiful. This portrait is also a reminder of my womanhood and how I should be empowered every day, because I am lucky to be able to express my femininity and be my own person, unlike some women who have come before me. Using oil paint on canvas, I was able to capture this. Paying close attention to all the details- even the little imperfections I may have wanted to skip over. In society’s eyes, I may not be the ideal vision of beauty, however to me, the artist, I am beautiful
Locally Tight Programs
Get PDFProgram completion is a translation from the language of logic programs into the language of first-order theories. Its original definition has been extended to programs that include integer arithmetic, accept input, and distinguish between output predicates and auxiliary predicates. For tight programs, that generalization of completion is known to match the stable model semantics, which is the basis of answer set programming. We show that the tightness condition in this theorem can be replaced by a less restrictive “local tightness” requirement. From this fact we conclude that the proof assistant ANTHEM-P2P can be used to verify equivalence between locally tight programs
From Script to Scene: A Directing Capstone
No full textThis demonstration showcases the process of how to take a written scene and guide it from the page to the performance utilizing both presentation and performance. Starting with an overview of the written play Witch by Jen Silverman, and a brief on the playwright, then moving into a discussion of the process of analyzing the script singularly as the director, the process of casting, and then digging into the script as a cast. In the final part of the demonstration, actors Kevin Bray and Emma Riley will perform a scene from the play. This presentation seeks to demonstrate how much goes into a performance even before actors receive their scripts
Subacute to Chronic Subdural Hematoma in an 18-Year-Old Male Football Player
No full textThe purpose of the report is to present the case of a high school football player who survived two brain surgeries to treat a subacute subdural hematoma that turned chronic (cSDH). This case proves to be unique due to the lack of mechanism, the age of the patient, the complications from surgery, and the recovery.9,12,16 The patient underwent an MMA (middle meningeal artery) embolization to treat the subacute hematoma, followed by a double burr hole craniotomy with drainage of chronic subdural hematoma. It is important for athletic trainers along with other members of the health care system to work as a team and to avoid tunnel vision when treating athletes for concussions as further pathologies may be present
Exploring Asynchronous Pronunciation Training Through Context-Aware Pronunciation Applications
Get PDFThis paper provides a survey of various research articles on context-aware asynchronous pronunciation training applications. First, a set of seven articles is reviewed and summarized. Next, they are synthesized over the three main topics of 1) automated speech recognition, 2) non-native speaker considerations in language learning, and 3) future directions for research and development within computer-assisted pronunciation training (CAPT). Research in the areas of acoustic and pronunciation modeling (both implicit and explicit), pedagogical considerations for CAPT application design, Goodness of Pronunciation algorithm scoring, accent recognition and neutralization, and more are discussed
Effects various distilled water brands have on Chlorophytum comosum.
Get PDFWhen first attempting home gardening, one of the challenges many home-renters are starting to face is being able to supply enough clean water to one’s plants. In order to overcome this challenge, many plant enthusiasts are utilizing prepackaged distilled water from price friendly brands available at most regional Walmart locations. With the number of choices available on the shelves of today’s grocery stores, and vague ingredient lists on packaging it can be challenging to determine which brand is actually best suited for one’s specific needs. In order to determine the best distilled water suited to grow Chlorophytum comosum, various gallons of distilled water manufactured by different companies will be used to treat the developing specimens. The effects of the distilled water on Chlorophytum comosum was observed over the selected growth period, and the relative dry weight of the roots was taken for analysis. After being weighed, the average dried root weight of Pure Life was 0.066 土 0.019 grams, which is 0.002 more than the root weight of the control, while the average root weight of the Parent\u27s Choice brand was 0.014 土 0.004 grams
Anti-thesis: When Your Worst Moments Become Your Best Work
Get PDFMy honors capstone project expands the creative work of a major writing assignment in English 3170: Successful Freelance Magazine Writing, which was modeled after Susan Shapiro’s “Humiliation Essay.” Shapiro’s signature assignment encourages students to write about an embarrassing or upsetting moment with the aim to force sincerity and humility. She writes, “It encourages students to shed vanity and pretension and relive an embarrassing moment that makes them look silly, fearful, fragile or naked.” The humiliation essay, she claims, often leads to publication because the conflict of the assignment inspires writers, and the narrator’s self-insight that occurs during the process of writing is appealing to editors and readers. My Humiliation Essay, “Poor Thing” is about the narrator\u27s experience with a date gone wrong, which inspired considerations of personal growth and identity.
After I completed the essay, I wrote a reflection concerning the writing process and information on publication. Sections include goals I had in mind writing the piece, what the publication process is like, and why one would feel incentivized to publish as an undergraduate. I apply some of these concepts to the essay I wrote and discuss my future goals as well
What makes us Good Leaders?
Get PDFWhat makes us good leaders? It’s a question that philosophers, politicians and business strategists alike have been asking for centuries. Generations of scholars have sought to pinpoint the various attributes and characteristics that define leadership beyond a formal organizational role. Going a step beyond, extensive research has also been devoted to deciphering what abilities make certain individuals successful as leaders in comparison to their peers, along with how aspiring leaders can practice these abilities to hone their own leadership performance. All of this research culminates in an intimidating amount of literature, riddled with a broad array of theories and conclusions regarding the most important leadership factors, many of which are contradictory. Even as experts continually seek to refine the concept of what the ideal leader looks like, the discussion surrounding leadership has noticeably shifted in recent years to emphasize a different set of organizational faculties such as employee wellbeing, participation, and culture. This further complicates one’s ability to find a synthesis between the various conflicting ideas.
It shall be the primary purpose of the following essay to contribute to this discussion, and, if appropriate, to render a conclusion as to the optimal set of leadership actions. It will begin by exploring the complicated history of leadership theory along with an overview of its most commonly regarded characterizations, both historically and in the present day. It will then take a more scientific approach by examining the lives and the levels of success of various real-world leaders in an effort to identify commonalities. Along the way it will investigate examples of both good and bad leaders in order to learn from their experiences in order to gain insight into what leadership characteristics are associated with organizational success. From there, it will attempt to narrow down a concrete list of the most important faculties of leadership based off of the preceding sections, incorporating additional data and outside research to back up these findings. Only then will it attempt to identify a comprehensive leadership theory that incorporates all the greatest advantages of the theories previously discussed, examining why such a comprehensive theory would lead to optimal performance for both the firm and its employees, and lastly how such a theory could be practically applied. Finally, the essay will conclude with a final discussion of the concept of leadership itself, along with the numerous difficulties involved in finding one all-encompassing leadership approach