I.M.B.Y. (in my backyard)

As future architects, it is our goal to use the poetry of built space to spark change within our communities. This must start by understanding the community and the history of existing neighborhoods. We can use this timeline and moments within as an expression of storytelling to influence structure and user type. Throughout the respected research areas, this begins to get depicted through the social discrimination of race, religion, and ethnicity. Although the United States is one of the most diverse countries in the world, our cities are still subdivided by the described discriminatory factors. This is due to prior segregation and the continuation of it through the industrial revolution. As our major cities expanded, the population grew around it full of life and community; however, as they began to collapse, the groups that were divided would become neglected leading to areas of abandonment and decay. These issues impact us today with social and environmental injustices. The existing community persists within these areas with strong-knit communities partnered alongside poor economic and social growth. This proposal is to provide a voice and allocated space for the immediate residents. Giving the local people an opportunity to exhibit their cultural identity with creation studios, public space, and culinary incubators. The goal behind this is to influence other developments down the adjacent corridors and into the immediate residential districts. As a resident of white decent, it is impossible for me to understand or experience the problems and discrimination embedded within/against different racial communities, but I believe it is my duty as a civil servant to recognize the existing issues with provided solutions for future growth. This proposal idealizes the welfare of the people.College of Architecture and PlanningThesis (B. Arch.

Protein secondary structure prediction: Creating a meta-tool

Abstract only availableProtein structure prediction is a growing field of interest for a many varied reasons, owing not only to its obvious utility, but also the success that applying newer mathematical tools has garnered in recent years. Despite the intractability of determining optimal protein structure directly by finding a lowest-energy conformation among a huge amount of candidates, many heuristic methods have emerged that sacrifice some degree of accuracy for reasonable speed of execution. Through the use of numerical techniques such as neural networks(1), neural networks bolstered by position-specific scoring matrices generated by psi-blast(2), and k-nearest neighbor algorithms(3), the success rate of protein structure prediction has been increasing over the past decade and a half. Each of these tools has particular strengths and weaknesses. To address this and to improve prediction accuracy, we are constructing a three-part meta-tool that combines k-nearest neighbor methods, neural network methods, and hidden markov models to predict the secondary structure of proteins based on their position-specific scoring matrices. The results from each of the individual tools will be integrated and filtered to form a final prediction. This tool will be available on the web through a simple interface for those wishing to evaluate or utilize it. References: 1: Rost and Sander. Predictions of protein secondary structure at better than 70% Accuracy; J. Mol. Biol. (1993) 232, 584-599 2: Jones. Protein secondary structure prediction based on position-specific scoring matrices; J. Mol. Boil. (1999) 292, 195-202 3: Bondugula, Duzlevski, Xu. Profiles and fuzzy k-nearest neighbor algorithm for protein secondary structure prediction; (unpublished).NSF-REU Program in Biosystems Modeling and Analysi

Synthesis of Sphingolipids Impacts Survival of Porphyromonas gingivalis and the Presentation of Surface Polysaccharides

Bacteria alter the biophysical properties of their membrane lipids in response to environmental cues, such as shifts in pH or temperature. In essence, lipid composition determines membrane structure, which in turn influences many basic functions, such as transport, secretion, and signaling. Like other members of the phylum Bacteroidetes, the oral anaerobe Porphyromonas gingivalis possesses the ability to synthesize a variety of novel membrane lipids, including species of dihydroceramides that are distinct, yet similar in structure to sphingolipids produced by the human host. The role of dihydroceramides in the physiology and pathogenic potential of the human microbiota is only beginning to be explored; yet there is increasing data indicating that these lipids play a role in human diseases, such as periodontitis and multiple sclerosis. Here, we report on the identification of a gene (PG1780) in the chromosome of P. gingivalis strain W83 encoding a putative serine palmitoyltransferse, the enzyme that catalyzes the first step in sphingolipid biosynthesis. While we were able to detect dihydroceramides in whole lipid extracts of P. gingivalis cells as well as crude preparations of outer membrane vesicles, sphingolipids were absent in the PG1780 mutant strain. Moreover, we show that the synthesis of sphingolipids plays an essential role in the long-term survival of the organism as well as its resistance to oxidative stress. Further, a PG1780 mutant displayed much lower activity of cell-associated arginine and lysine gingipains, yet slightly higher activity in the corresponding culture supernates, which we hypothesize is due to altered membrane properties and anchoring of these proteases to the cell surface. In addition, we determined that sphingolipid production is critical to the presentation of surface polysaccharides, with the mutant strain displaying less K-antigen capsule and more anionic polysaccharide (APS). Overall, we have discovered that, in addition to their role in pathogenicity, the synthesis of sphingolipids is critical to the cellular homeostasis and persistence of this important dental pathogen

Teleological essentialism across development

Do young children have a teleological conception of the essence of natural kinds? We tested this by examining how the preservation or alteration of an animal’s purpose affected children’s persistence judgments (N = 40, ages 4 - 12, Mean Age = 7.04, 61% female). We found that even when surface-level features of an animal (e.g., a bee) were preserved, if the entity’s purpose changed (e.g., the bee now spins webs), children were more likely to categorize the entity as a member of a different natural kind (e.g., a spider) and these effects were similar in magnitude to altering the surface-features of a natural kind. Our results suggest that we might view teleological properties as partially constitutive of the essence of natural kinds

Genome Sequences of 18 Salmonella enterica Serotype Hadar Strains Collected from Patients in the United States

Despite being linked to a number of recent poultry-associated outbreaks in the United States, few reference genomes are available for Salmonella enterica serotype Hadar. Here, we address this need by reporting 18 Salmonella Hadar genomes from samples collected from patients in the United States between 2014 and 2020

Crystal Structure of an LSD-Bound Human Serotonin Receptor

SummaryThe prototypical hallucinogen LSD acts via serotonin receptors, and here we describe the crystal structure of LSD in complex with the human serotonin receptor 5-HT2B. The complex reveals conformational rearrangements to accommodate LSD, providing a structural explanation for the conformational selectivity of LSD's key diethylamide moiety. LSD dissociates exceptionally slow from both 5-HT2BR and 5-HT2AR—a major target for its psychoactivity. Molecular dynamics (MD) simulations suggest that LSD's slow binding kinetics may be due to a "lid" formed by extracellular loop 2 (EL2) at the entrance to the binding pocket. A mutation predicted to increase the mobility of this lid greatly accelerates LSD's binding kinetics and selectively dampens LSD-mediated β-arrestin2 recruitment. This study thus reveals an unexpected binding mode of LSD; illuminates key features of its kinetics, stereochemistry, and signaling; and provides a molecular explanation for LSD's actions at human serotonin receptors.PaperCli

Afterimage

https://via.library.depaul.edu/museum-publications/1007/thumbnail.jp

Izu-Bonin-Mariana Rear Arc: The Missing Half of the Subduction Factory

4GT) lies in the western part of the Izu fore-arc basin, ~60 km east of the arc-front volcano Aogashima, ~170 km west of the axis of the Izu-Bonin Trench, 1.5 km west of Ocean Drilling Program (ODP) Site 792, and at 1776 meters below sea level (mbsl). It was drilled as a 150 m deep geotechnical test hole for potential future deep drilling (5500 meters below seafloor [mbsf]) at proposed Site IBM-4 using the D/V Chikyu. Core from Site U1436 yielded a rich record of Late Pleistocene explosive volcanism, including distinctive black glassy mafic ash layers that may record large-volume eruptions on the Izu arc front. Because of the importance of this discovery, Site U1436 was drilled in three additional holes (U1436B, U1436C, and U1436D), as part of a contingency operation, in an attempt to get better recovery on the black glassy mafic ash layers and enclosing sediments and to better constrain the thickness of the mafic ash layers. IODP Site U1437 is located in the Izu rear arc, ~330 km west of the axis of the IzuBonin Trench and ~90 km west of the arc-front volcanoes Myojinsho and Myojin Knoll, at 2117 mbsl. The primary scientific objective for Site U1437 was to characterize “the missing half of the subduction factory”; this was because numerous ODP/Integrated Ocean Drilling Program sites had been drilled in the arc to fore-arc region (i.e., ODP Site 782A Leg 126), but this was the first site to be drilled in the rear part of the Izu arc. A complete view of the arc system is needed to understand the formation of oceanic arc crust and its evolution into continental crust. Site U1437 on the rear arc had excellent core recovery in Holes U1437B and U1437D, and we succeeded in hanging the longest casing ever in the history of R/V JOIDES Resolution scientific drilling (1085.6 m) in Hole U1437E and cored to 1806.5 mbsf

Researching COVID to Enhance Recovery (RECOVER) Adult Study Protocol: Rationale, Objectives, and Design

IMPORTANCE: SARS-CoV-2 infection can result in ongoing, relapsing, or new symptoms or other health effects after the acute phase of infection; termed post-acute sequelae of SARS-CoV-2 infection (PASC), or long COVID. The characteristics, prevalence, trajectory and mechanisms of PASC are ill-defined. The objectives of the Researching COVID to Enhance Recovery (RECOVER) Multi-site Observational Study of PASC in Adults (RECOVER-Adult) are to: (1) characterize PASC prevalence; (2) characterize the symptoms, organ dysfunction, natural history, and distinct phenotypes of PASC; (3) identify demographic, social and clinical risk factors for PASC onset and recovery; and (4) define the biological mechanisms underlying PASC pathogenesis. METHODS: RECOVER-Adult is a combined prospective/retrospective cohort currently planned to enroll 14,880 adults aged ≥18 years. Eligible participants either must meet WHO criteria for suspected, probable, or confirmed infection; or must have evidence of no prior infection. Recruitment occurs at 86 sites in 33 U.S. states, Washington, DC and Puerto Rico, via facility- and community-based outreach. Participants complete quarterly questionnaires about symptoms, social determinants, vaccination status, and interim SARS-CoV-2 infections. In addition, participants contribute biospecimens and undergo physical and laboratory examinations at approximately 0, 90 and 180 days from infection or negative test date, and yearly thereafter. Some participants undergo additional testing based on specific criteria or random sampling. Patient representatives provide input on all study processes. The primary study outcome is onset of PASC, measured by signs and symptoms. A paradigm for identifying PASC cases will be defined and updated using supervised and unsupervised learning approaches with cross-validation. Logistic regression and proportional hazards regression will be conducted to investigate associations between risk factors, onset, and resolution of PASC symptoms. DISCUSSION: RECOVER-Adult is the first national, prospective, longitudinal cohort of PASC among US adults. Results of this study are intended to inform public health, spur clinical trials, and expand treatment options