bluuebunny/crossref_metadata_2025 huggingface dataset:
The role of CYP46A1 and its metabolic product, 24S-hydroxycholesterol, in Neuro 2A cell death
Authors: Ni Allen , Jiang Xiangning
Published: September 2023

Cholesterol is a major component of neuronal cell membrane and myelin sheath. Therefore, maintaining cholesterol homeostasis is crucial for brain functioning and development. Brain cholesterol is synthesized de novo. To achieve homeostasis, excess cholesterol is removed by its conversion into 24S-hydroxycholesterol (24S-HC), which crosses the blood-brain barrier to enter the blood stream for clearance. This conversion is facilitated by the brain-specific protein, CYP46A1 (cholesterol 24-hydroxylase). Previous studies reported that hypoxia-ischemia caused disruption of cholesterol homeostasis. Increases of CYP46A1 and 24S-HC in neonatal mouse brain correlated with hypoxicischemic brain damage. Blood level of 24S-HC was also elevated and is a potential diagnostic biomarker for brain damage severity. However, how CYP46A1 and 24S-HC are functionally involved in neuronal cell death is unknown. Finding the direct effect of CYP46A1 and 24S-HC on brain cell damage will help assess the possibility of using 24S-HC for brain damage diagnosis. We hypothesized that hypoxiaischemia upregulated CYP46A1 expression, leading to an increase in 24S-HC, thus triggering cell death. In this study, we either transfected Neuro 2A cells with CYP46A1 cDNA or treated the cells with 24SHC. Cell viability was measured to evaluate their effect on cell damage. Cells expressing CYP46A1 had significantly less viability compared to the negative control. Up to 55% reduction in cell viability was also observed in 24S-HC-treated cells. This work supports that CYP46A1 and 24S-HC could directly trigger cell death. The direct involvement of 24S-HC in cell death provides further evidence that 24S-HC can be a promising biomarker for diagnosing brain damage severity.
Culturally Adapted Assessment Tool for Autism Spectrum Disorder and its Clinical Significance
Authors: Das Anwesha , Ray Aranyo
Published: September 2023

Diagnosing of Autism Spectrum Disorder (ASD) using tools developed in the West is challenging in the Indian setting due to a huge diversity in sociocultural and economic backgrounds. Culturally adapted tools, such as the International Clinical Epidemiology Network (INCLEN) Diagnostic Tool for Autism Spectrum Disorder, have been developed in several Indian languages, yet, they do not accommodate all verbal abilities and education backgrounds. To address this disparity, we developed a home-based, audiovisual game app (Autest) suitable for ASD risk assessment in Indian children under 10 years of age. The game has five modules for each age group with specific peer interaction and play skill assessments. Each module follows a story from the Panchatantra, a popular Indian story series for children. Gameplay and behavior are tracked to assess risk. The effectiveness of Autest was rated by 30 psychologists with respect to current tools. Ratings suggested that the tool is effective and can reduce social inhibition and facilitate assessment due to the lack of a language barrier using emojis, cultural appropriateness, ease of administration, and simple scoring. This tool is particularly useful minimally verbal, at-risk children. Further usage and development of Autest can improve risk assessment and early intervention measures for children with ASD in India.
Dune flora can emerge from seed islands (Concon, Chile)
Authors: Faras Giusti-Bilz Josefa , Elrtegui Francioli Sergio
Published: September 2023

The study of species within natural communities, which has progressed remarkably in recent decades, is of great interest in the field of ecology. Through the process of characterizing dunes, mounds of sand formed by the wind, and their plant communities we can get to know the physiognomy and floristic composition of the territory. However, little is known about how these plant communities originate. Based on the hypothesis that dune flora can emerge from seed islands: holes in the sand 6 cm deep containing a mixture of seeds, broken branches of shrubbery, and rabbit feces, during spring, we determined the composition of 20 seed islands in the sand dunes of Concon, Chile and measured how many seeds germinated in each one. In support of our hypothesis, we found that, on average, four seeds germinated in each seed island.
The Perks of Watching a Movie: How the Portrayal of Anxiety and Depression in Film Affects Teenagers’ Perception of Anxiety and Depressive Disorders
Authors: Wolcott Joelyz , Kurtz Brianna
Published: September 2023

In film, anxiety and depressive disorders are often depicted inaccurately. When viewers are exposed to these inaccurate portrayals, they collect misinformation about the disorders, as well as people who live with them, leading to stigma. This study used a mixed-method descriptive approach to analyze 16 teenagers’ attitudes towards people with anxiety and depression. We then compared these results to their attitudes towards the character Charlie in the coming-of-age film The Perks of Being a Wallflower, who has clinical anxiety and depression. Participants were given an initial survey, shown clips from the film, then given a reflection survey. They were also asked their thoughts on the depiction of anxiety and depression in film as a whole and its implications. We hypothesized that participants would develop a more negative opinion of people with anxiety and depressive disorders after watching the film as compared to their initial survey because characters with mental illnesses are most often depicted as violent and unable to lead a normal life. The results did not support our hypothesis. We found that participants used more adjectives with positive connotations to describe the character Charlie than they had used to describe someone with anxiety and depression. Additionally, while participants understood how these portrayals create stigma, they did not attribute this to misinformation. These results can be used to help both the film industry and the movie-going public better understand the effects of inaccurate storytelling and the extent to which it informs public perception.
Predicting Orbital Resonance of 2867 Šteins Using the Yarkovsky Effect
Authors: Rosenberg Will , Herrera-Vendrell Esteban , Nucuta Raymond , Wahal Karsen , Bhardwaj Sarthak , Gallie William Bryce , McClernon Paul
Published: September 2023

While gravitational forces have the largest impact on asteroid orbit determination, thermal forces such as the Yarkovsky and YORP effects also perturb asteroid orbits. We analyzed the impact of these thermal effects on the orbit of asteroid 2867 Šteins, an E-type asteroid measuring five kilometers in diameter. The orbit of Šteins lies within the range of a Kirkwood Gap, a region devoid of asteroids because of Jupiter’s gravitational pull. Given that thermal effects can perturb asteroids of similar properties, we sought to determine whether the Yarkovsky effect would push Šteins into a Kirkwood Gap within 50,000 years. Based on Šteins’ location and size, we hypothesized that the Yarkovsky effect will push Šteins into a Kirkwood gap. We computationally generated a thermal map of Šteins to approximate the Yarkovsky force and YORP torque. Analysis of the thermal map yielded an average Yarkovsky force parallel to velocity of -0.714 N and acceleration of -5.22 x 10-15 m/s2. The torque parallel to the angular velocity due to the YORP effect was 4.680 N m, with an angular acceleration of 1.217 x 10-20 rad/s2. We inputted the calculated Yarkovsky force into NASA’s GMAT to model the resulting change to Šteins’ orbit and found that the Yarkovsky force decays the semi-major axis of Šteins by 16.4 km in 242.2 years, and up to 5,365 km in 50,000 years within 95% confidence. This perturbation is unlikely to transfer Šteins into a Kirkwood Gap.
Access to public parks, drinking fountains, and clean public drinking water in the Bay Area is not driven by income
Authors: Zaroff Eliza , Holmquist Anna
Published: September 2023

Access to green space—an area of grass, trees, or other vegetation set apart for recreational or aesthetic purposes in an urban environment—and clean drinking water can be unequally distributed in urban spaces, which are often associated with income inequality. Little is known about public drinking water and green space inequities in the Bay Area. For our study, we sought to understand how public park access, drinking fountain access, and the quality of public drinking water differ across income brackets in the Bay Area. We hypothesized that there would be a significant positive correlation between income and the number of drinking fountains, the number of parks, and drinking fountain water quality. For each Bay Area sub-region, we analyzed water samples from four drinking fountains from four different ZIP codes, and recorded the number of parks and fountains in relation to income for eight different ZIP codes. On a large scale, water quality, determined by presence of chemical compounds and other contaminants, was generally high, and there was no significant relationship between income and fountain access, and income and fountain water quality. Though we observed smaller-scale instances of inequalities, in the park distribution in the Bay Area as a whole, and in the Southern Bay’s water quality and park distribution, our results indicate that other factors could be influencing water quality, and park and fountain access in the Bay Area.
The effects of UV-C and ionizing radiation on the functions of Escherichia Coli
Authors: Kaki Saket , Bartley Mathew , DeVoss Rebecca
Published: September 2023

Planetary protection is an extremely important consideration for spacecraft missions to other planets and worlds, especially those that may harbor life. This work presents the effects of Ultraviolet (UV) C and ionizing radiation on Escherichia coli (E. coli) bacteria in order to characterize the behavior of bacteria in space to better inform planetary protection considerations. We sent a sample of E. coli K-12, a commonly available strain, on a NASA sounding rocket to space via the Cubes In SpaceTM program, a global competition that allows students to design and propose experiments that launch on a sounding rocket. Our hypothesis was that the ionizing and UV-C radiation experienced during rocket launch and spaceflight will negatively affect the cellular functions of the E. coli bacteria and kill some bacterial cells but will not exterminate the entire culture of bacteria. Our experiment demonstrated that the number of colony forming units (CFUs) in the space sample was lower than the control sample. Thus, we suggest that the UV-C and ionizing radiation experienced during rocket launch negatively affects the cellular functions of E. coli.
Effects of airport runoff pollution on water quality in bay area sites near San Francisco and Oakland airports
Authors: Walters Elisabeth , Spuller Kerri
Published: September 2023

Airports contribute to pollution through point source and non-point source pollution, which can have negative effects on water quality and aquatic life. The purpose of our study was to determine if runoff pollution from the San Francisco airport (SFO) and Oakland airport (OAK) impacts water quality in the San Francisco Bay Area. We tested water quality at 12 sites surrounding these two airports, specifically testing for pH and the presence of specific metals and nitrates. From our results, we found that the presence of zinc, copper, chromium and nitrate increased as we got closer to the airports. The pH remained constant throughout the sites. We concluded that airport pollution is a likely source of elevated concentrations of some heavy metals and nitrates in the San Francisco Bay Area.
Motion tracking and analysis of spray water droplets studied by high-speed photography using an iPhone X
Authors: Geng Jenny , Geng John
Published: September 2023

Smartphones are not only becoming an inseparable part of our daily lives, but also a low-cost, powerful optical imaging tool for more and more scientific research applications. In this work, we hypothesized that some smartphones could be used as a low-cost, high-speed, photographic alternative to expensive equipment, such as those typically found in scientific research labs, to accurately perform motion tracking and analysis of fast-moving objects. This demonstrative experiment was done at home at very low cost by using a low-power green laser (<0.1 W) purchased from Amazon, an iPhone X, and a water spray bottle. The sprayed water droplets were illuminated by a divergent green laser beam and recorded with a smartphone using the Slow-Motion Video function (240 frames per second), which allows us to record high-speed events. The Slow-Motion Video was converted to a series of consecutive images taken every 1/240 second (or 4.16 ms), enabling tracking and motion analysis of the sprayed water droplets. By analyzing these consecutive images, the speed and flight trajectory of water droplets in the air were obtained, thereby enabling us to estimate the area of the water droplets landing on the ground.
Role of Environmental Conditions on Drying of Paint
Authors: Aggarwal Deepti , Dutta Riya , Dutta Bhaskar
Published: September 2023

Most manufacturing industries paint their products to protect them from environmental degradation and enhance aesthetics. Reducing paint drying time is an important step in improving production efficiency and reducing costs. To find the most effective way to dry paint, we performed a series of 60 experiments by varying different environmental conditions: humidity, lighting, substrate roughness, and paint color. We hypothesized that decreased humidity would lead to faster drying, ultraviolet (UV) light exposure would not affect the paint colors differently, white light exposure would allow for longer wavelength colors to dry at a faster rate than shorter wavelength colors, and substrates with higher roughness would dry slower. We constructed a custom paint booth to control the environmental conditions for a variety of painted samples and regularly weighed the samples to monitor the drying rate. Our experiments showed that trials under high humidity dried slightly faster than trials under low humidity, contrary to the hypothesis. We found that white paint had the slowest drying rate compared to red, yellow, and blue paints under ambient and white light, while under UV light the drying rate of all paints were similar to one another. Colored paints dried the fastest on a metal substrate followed by canvas and then wood, following the increase in roughness of the substrate. Overall, our studies show that the paint drying process is very much dependent on its surrounding environment, and optimizing the drying process requires a thorough understanding of the environmental factors and their interactive effects with the paint constituents.
Detection and Control of Spoilage Fungi in Refrigerated Vegetables and Fruits
Authors: Chari Sadhana , Xie Katherine , Kale Isha , Khow Kimberly , Nair Ria , Mikhail Hanna Nardeen
Published: September 2023

Post-harvest infection of fruit and vegetable products is an ever-growing issue in the food industry. About 20% of all produced fruits and vegetables are lost each year due to spoilage. Some sources of spoilage are mycotoxin-producing fungi, which can cause serious health threats in humans, from acute poisoning to long-term effects such as cancer. Therefore, using preservatives to avoid contamination and the eventual production of mycotoxins in our food is essential. However, synthetic preservatives appear to be harmful to human health and the environment, making it favorable to replace them with natural and safer preservatives. Using the essential oils of aromatic plants as preservatives has been found to help prevent the deterioration of food. This work aimed to isolate and identify some of the filamentous fungi that contaminate refrigerated fruits and vegetables. We studied the effect of eugenol essential oil and its derivative, acetyl isoeugenol, at three different concentrations and temperatures on the fungal growth of two isolated fungal species. Our experiments revealed that eugenol was the better choice as an antifungal agent against the two tested fungi: Cladosporium cladosporioides and Penicillium italicum. The inhibition effect of both tested oils against fungal growth was concentration-dependent, independent of any changes in temperature. However, further work on eugenol derivatives and their effects on both fungi and vegetables and fruits is still needed.
Effect of mass and center of gravity on vehicle speed and braking performance
Authors: Tian Jack , Whitfield Clifford
Published: September 2023

The center of gravity (CG) of a vehicle is a key parameter that helps determine vehicle stability, braking efficiency, and safety. In a gravity vehicle, the mass of the vehicle is also an important factor in vehicle performance because it provides the sole force of propulsion. We hypothesized that if a vehicle was constructed according to mathematically-derived optimal mass and CG location, then a fast and accurate vehicle would result. To test this hypothesis, we constructed a gravity vehicle, which is a vehicle powered by its own gravity on a ramp. Mathematical calculations were used to rationalize this hypothesis. Shifting the CG rearward increased the vehicle’s effective launching height on the ramp and corresponding gravitational potential energy, resulting in greater kinetic energy and speed. However, the accuracy (m-1), defined as the reciprocal of braking distance from the target, increased initially, peaked, and then decreased as the vehicle mass increased. We performed experiments with five mass parameters and three load locations, using an unloaded vehicle as control. Speed and accuracy were then measured for 16 sets of data. Compared to front and centrally-loaded vehicles, the rear-loaded vehicles displayed the best results. As the mass increased to a medium value, both the speed and accuracy reached a maximum. The experimental results supported the hypothesis that the optimal CG position is 22 ± 1 cm rear of the front axle and the ideal mass is 867 ± 50 grams. This study highlights the significance of CG position in vehicle design.
Exercise, grades, stress, and learning experiences during remote learning due to the COVID-19 pandemic
Authors: Lu Marco , Mo Davis , Du Fei
Published: September 2023

During the COVID-19 pandemic, because of social distancing measures, schools had to deliver classes through remote learning. The purpose of this study is to understand the relationships between grades, exercise, stress, and students’ learning experience for middle and high school students during this remote learning period. Based on prior literature, we hypothesized that exercise would reduce stress during the remote learning period. We also hypothesized that receiving grades during the remote learning period would increase stress but also enhance students’ perceived remote learning experience. To test our hypotheses, we conducted a survey of middle and high school students across different states in the United States. We asked participants to rate what they thought about their levels of stress and remote learning experience during the COVID-19 pandemic. We found that, on average, middle and high school students experienced similar stress levels during the remote learning period due to the COVID-19 pandemic compared to the pre-COVID-19 period. We also found that, on average, middle and high school students’ perceived learning experience was lower during the remote learning period due to the pandemic compared to the pre-COVID-19 period. Consistent with our hypotheses, we found that physical exercise helped reduce stress during the remote learning period. We also found that receiving grades for schoolwork increased students’ stress and effort during the remote learning period but did not have a significant impact on students’ learning experience. Furthermore, we found a significant negative relationship between students’ stress and their perceived learning experience.
Reducing PMA-induced COX-2 expression using a herbal formulation in MCF-7 breast cancer cells
Authors: Nair Maanasi Vinay , Umrao Ankita , Rao Gururaj A , Rao Jyothsna A
Published: September 2023

Cyclooxygenase-2 (COX-2) is the inducible form of a group of enzymes that catalyze the conversion of arachidonic acid to prostaglandins. This isoform is often overexpressed in breast cancer cells. COX-2 overexpression correlates with an aggressive phenotype in breast cancer, including higher histological grade, larger tumor size, estrogen receptor (ER) negativity, and human epidermal growth factor receptor 2 (HER-2)/neu positivity. Another study, via molecular, animal, and human investigations, supported that COX-2 expression increases as cancer develops, getting progressively worse during the metastatic phase through the release of vascular endothelial growth factor (VEGF). Traditional medicine or herbal compounds have been gaining increasing popularity for alternative treatment for cancer alone and in conjunction with treatments. Green tea and turmeric are famous for their numerous beneficial effects on the body, including anti-oxidative, chemo-preventive, chemo-protective, anti-inflammatory properties. COX-2 expression was induced using phorbol-12-myristate-13-acetate (PMA). This study tested the effect of the herbal formulation HF1 (mainly composed of (-)-epigallocatechin-3-gallate (EGCG) and curcumin) on the COX-2 mRNA levels in the breast cancer cell line MCF-7. We hypothesized that PMA-induced overexpression of COX-2 in MCF7 cells would be eliminated after exposure to HF1. PMA increased COX-2 levels by 3-fold as compared to the untreated MCF-7 culture (no PMA, no HF1). However, when cells were treated with HF1 alongside PMA, we observed a 60% decrease in COX-2 levels.
Impact of dams in Santa Clara County on the nitrification of the surrounding ecosystem
Authors: Vazhaeparambil Thresiamma , Spuller Kerri
Published: September 2023

Two dams in Santa Clara County were studied in order to determine how they impacted the nitrification rates of their surrounding ecosystems. Based on this information, the results were used to discern whether there were any correlations between the water conductivity, total dissolved solids, size, and age of the dams. We hypothesized that if the dams were impacting the nitrification rates in their ecosystems, then the nitrification rates would be higher upstream of the dams than downstream of the dams. We found that the soil nitrate levels are lower downstream than they are upstream, supporting other research that claims that dams can alter the nitration cycle of their surrounding environment.
Herbal formulation, HF1 diminishes tumorigenesis: a cytokine study between MCF-7 and BM-MSCs.
Authors: Guru Aeka Lakshmi , Umrao Ankita , Kasture Pooja V , Prasad Shambhavi , Rao Jyothsna , Rao Gururaj
Published: September 2023

Tumorigenesis is a result of favorable interactions between the tumor microenvironment (TME) and tumor cells. The microenvironment hosts several cytokines, soluble factors, and signaling factors secreted by stromal cells which accelerate the progression of cancer. Bone marrow mesenchymal stem cells (BM-MSCs) invade the TME and are hypothesized to differentiate into cancer associated fibroblasts (CAFs) by the action of Transforming growth factor beta (TGF-β) and Vascular Endothelial growth factor VEGF, some of the key cytokines involved in this process.

This study aimed to investigate expression of cytokines with different conditioned media using the MCF-7 breast cancer cell line and BM-MSCs. Furthermore, we also studied the effectiveness of a herbal formulation (HF-1) in countering the expression of these cytokines. BM-MSCs secreted significantly higher concentrations of the cytokines when in co-culture with MCF-7 cells. Furthermore, the diminished concentrations of VEGF and TGF-β observed post-addition of HF-1 demonstrates its potential applications in preventing tumorigenesis and cancer metastasis.
Novel biaryl imines and amines as potential competitive inhibitors of dihydropteroate synthase
Authors: Chang Warren , Rajaram Vigasini , Yallampalli Harshith , Dong Arielle , Huang Kimberly , Valiveru Anirudh , Njoo Edward
Published: September 2023

Antibiotic-resistant bacteria account for over 2.8 million infections and 35,000 deaths annually in the United States. The evolution of new resistant strains necessitates the continued development of new antimicrobial compounds. A target for further pharmaceutical development is the enzyme dihydropteroate synthase (DHPS), which plays a key role in prokaryotic biosynthesis of folic acid. A class of drugs called sulfonamides, including drugs sulfamethoxazole and sulfatrim, bind and act as competitive substrates to p-aminobenzoic acid (pABA), a substrate of DHPS, but are limited by their numerous side effects on the human body and bacterial resistance mutations that block larger molecules from entering the binding pocket. Here, we report the design, combinatorial synthesis, and antibacterial properties of a library of novel biaryl small molecules to target the binding pocket of DHPS. We hypothesize that the synthesized compounds in this study will have strong antibiotic efficacy because of their structural similarities to dihydropteroate, an intermediate in the biosynthesis of folate by the enzyme DHPS. Compounds were first screened in silico via docking to the binding pocket in DHPS. The antibiotic efficacy of these compounds was then tested on three species of bacteria related to human pathogens through a Kirby Bauer assay. Two hit compounds were discovered as having larger radii of inhibition compared to other compounds from the data of the assay. The larger radii of inhibition indicates that the bacteria tested against were susceptible to the use of the hit compounds. The results of the assay establish a definitive structure-activity relationship for the compounds studied and provide a basis for the future development of antibiotics targeting DHPS.
The effects of container materials on food microwave heat times
Authors: Frankiewicz Piper , Wollschlaeger Mark
Published: September 2023

The purpose of this study was to determine which material of container heats food the fastest in the microwave: plastic, glass, or ceramic. By finding out this information, microwave cooking times could be shortened, which would reduce money spent on electricity bills since the microwave would be running for less time. To conduct this study, a set amount of water and Campbell’s condensed tomato soup were heated in the microwave in a cup and a bowl of the various materials. After heating, the temperature change (°F) was measured and averaged for each container. We hypothesized that a plastic container would cause the food to heat the fastest because plastic is often not as thick as glass and ceramic. We observed that the ceramic cup and the glass bowl heated the fastest in their respective categories for both the water and tomato soup. Additionally, we also noted that bowls heated water and tomato soup faster than the cups. This implies that there are other factors that affect the heating times of food in the microwave, such as container surface area and mass. In conclusion, the data collected supports that there is a significant difference in cooking times between the different container materials that food is microwaved in.
Ribosome distribution affects stalling in amino-acid starved cancer cells
Authors: Deng Mark , Nofal Michel
Published: September 2023

Protein synthesis is a process central to all life on Earth, including mammalian cells. During this process, ribosomes attach to mRNA strands and translate them into proteins using amino acids. Under stress (for example, when the supply of circulating amino acids has been disrupted by tissue injury), ribosomes can stall. Ribosome profiling, a technique that creates a snapshot of active ribosomes in a cell by sequencing ribosome-protected mRNA fragments, captures a snapshot of ribosomes along transcripts and can detect such stalling events. This method has also revealed that the patterns of ribosomes along transcripts can vary from transcript to transcript in a manner that has not yet been explained. Here, we analyzed ribosome profiling data from amino acid-starved pancreatic cancer cells to explore whether the pattern of ribosome distribution along transcripts under normal conditions can predict the degree of ribosome stalling under stress. We hypothesized that ribosomes would stall more along “elongation-limited” transcripts that have fewer ribosome footprints near the start and stop codons than “initiation-limited” transcripts that have a large fraction of footprints at the start codon. Indeed, we found that ribosomes in amino acid-deprived cells stalled more along elongation-limited transcripts. By contrast, we observed no relationship between read density near start and stop and disparities between mRNA sequencing reads and ribosome profiling reads. This research identifies an important relationship between read distribution and propensity for ribosomes to stall, although more work is needed to fully understand the patterns of ribosome distribution along transcripts in ribosome profiling data.
Design and in silico screening of analogs of rilpivirine as novel non-nucleoside reverse transcriptase inhibitors (NNRTIs) for antiretroviral therapy
Authors: Wu Jeslyn , Luk Charissa , Zhou Catherine , Shah Aashi , Yuvaraj Aishwarya , Njoo Edward
Published: September 2023

Part of the retroviral genus, the human immunodeficiency virus (HIV) relies on the host’s cellular machinery for replication. The viral genetic material is composed of ribonucleic acid (RNA) which, upon delivery into the host’s cells, is reverse transcribed into deoxyribonucleic acid (DNA) by the viral enzyme reverse transcriptase (RT). This is then used for the production of new viral components, thus allowing for further replication and spread of HIV. Because this virus selectively targets CD4+ T cells, the infection inevitably leads to weakening of the host’s immune system, which can then lead to acquired immunodeficiency syndrome (AIDS). One treatment for HIV is non-nucleoside reverse transcriptase inhibitors (NNRTIs), which are allosteric inhibitors of RT that disable the enzyme’s activity and thus viral replication. Previous NNRTIs approved for clinical use by the United States Food and Drug Association (FDA) include etravirine, doravirine, and rilpivirine. However, resistance to these drugs through mutations in RT necessitates the continued development of NNRTIs. Here, the structure of rilpivirine, a relatively recently FDA approved NNRTI, was used to design a library of analogs that were then evaluated in silico via high-throughput virtual screening (HTVS). From this, several structures were identified as potential next-generation NNRTIs with comparable predicted binding affinities to the allosteric binding pocket in RT as rilpivirine.
The impact of Red 40 artificial food dye on the heart rate of Daphnia magna
Authors: Inampudi Samay , Schwab Megan , Srivastava Annika , Inampudi Rao
Published: September 2023

Due to its relatively new appearance in foods, not many studies have been conducted on the effects of Red 40 food dye, therefore one aspect of its effects on the body should be explored. Red 40 is a chemical present in thousands of consumer products that poses potential health risks with one’s heart rate and hemoglobin functioning. The purpose of this study was to examine the effects of Red 40 food dye on the cardiac activity of Daphnia magna, a 2 mm long freshwater crustacean. We hypothesized that a higher concentration of Red 40 dye would result in an increased heart rate and activity in the Daphnia magna because of a need for increased oxygen intake, due to Red 40’s impact on hemoglobin molecules. D. magna were placed into Petri dishes containing Red 40 solutions ranging from 0% to 5% concentrations for five minutes. At the five-minute mark, the specimens were transferred to a glass slide and placed under a microscope to record their heart rates. The recorded video was slowed down to count the heart rate of each specimen, and the data was recorded. The results showed that as the concentration of the Red 40 solution increased, so did the heart rate and activity level of the specimen. We noticed the D. magna becoming more active and sporadic when concentrations increased as well.
An analysis of junior rower performance and how it is affected by rower's features
Authors: Biller Audrey , Samatova Nagiza
Published: September 2023

High-school student participation in rowing has increased over the last two decades. Due to the physical intensity of rowing, this sport may be expected to be male dominant while the female lightweight category may be expected to be non-competitive. Over the years, junior rowers may have become faster, and they may be expected to demonstrate their largest improvement by age 16. The purpose of this study was to test these expectations with hypothesis-driven experiments while presenting a glimpse into the world of high-school rowing by analyzing World Indoor Rowing Championship data. This dataset was obtained from ergometer machines used for rowing on land. The analysis showed that the participation of junior women has been exceeding the participation of junior men in the heavyweight class. We found that the key feature determining the performance of a rower is first sex and then weight class, but it is possible for a female rower to be faster than a male rower. Rowing has become more competitive in all categories except male heavyweight. We tested whether a junior rower achieves the largest ergometer time improvement by age 16 and accepted this hypothesis except for the female lightweight rowers. Additionally, for each category, we built the 2000-meter ergometer time distribution, which junior rowers can use to assess current performance and understand what they should achieve for top placement. Finally, we developed models predicting future ergometer times based on current performance, sex, weight class, and target percentile rank to guide junior rowers in their journey.
Solving a new NP-Complete problem that resembles image pattern recognition using deep learning
Authors: Abraham Naod , Kwok Alan
Published: September 2023

In computer science, non-deterministic polynomial time (NP) denotes the set of problems for which a solution, if it exists, can be checked quickly. We also call the set of problems in NP that are at least as hard as any other NP problem non-deterministic polynomial time complete (NP-complete). Although not known if they can be solved quickly as of writing this paper, NP-complete problems can be converted into one another quickly. A prominent and practical example is the protein folding problem, which is a problem of determining the shape and function of proteins. Some models of the protein folding problem have been shown to be NP-complete. In this paper, we discovered and provided a mathematical proof of a new NP-complete problem, that we named 3-Grid Pattern Decision Problem (3- GPDP). 3-GPDP is a decision problem that asks if a specific kind of pattern exists or not on a grid/matrix of numbers consisting of zeros and ones, much like image recognition. We hypothesized that a neural net would be able to solve 3-GPDP problems with high accuracy and low loss when trained. In support of our hypothesis, our experiment resulted in a neural net that performed with 84% accuracy and 0.14 loss without underfitting or overfitting. Moreover, there was also an increase in accuracy and decrease in loss with more training data. Hence, this further experimentally supported that using neural-networks can be a good heuristic approach to solve many NP-complete problems.
Willingness to visit the pediatric dentist during the COVID-19 pandemic
Authors: Rossitch Charles Michael , Adams Emily , Rossitch Michael
Published: September 2023

The COVID-19 pandemic has introduced many issues to healthcare. Many people, including children,

are missing important appointments because they are viewed as nonessential. Pediatric dentist appointments are a possible example of a commonly missed appointment since many parents do not view dental care as vital. The purpose of this study was to determine how the COVID-19 pandemic has affected parents’ willingness to allow their children to visit a suburban Atlanta pediatric dental practice and what safety measures make parents feel more comfortable about their children visiting the dentist. We hypothesized that parents would be less willing to allow their child to visit the dentist due to anxiety caused by the COVID-19 pandemic. The data showed a weak positive correlation between parents’ unwillingness to allow their child to visit the dentist and the COVID-19 pandemic. However, the majority of parents would allow their child to visit the dentist because anxiety towards visiting the dentist during the pandemic was found to be low. An electronic survey collected data on parents’ anxiety towards the pandemic and going to the dentist during the pandemic, safety measures that would make them more comfortable going to the dentist, and demographic information. Data were analyzed using risk ratio (RR) tables. We counted and categorized the responses, learning that protective gear (like masks) was the most commonly requested safety measure. Dentists can use this information to increase parents’ willingness to bring their children to the dentist.
Prediction of molecular energy using Coulomb matrix and Graph Neural Network
Authors: Hazra Rishi , Hazra Prasenjit
Published: September 2023

Molecular energy is used to estimate the overall favorability of the formation of a molecule, which can be measured either directly or indirectly. However, both methods require a chemical reaction. Molecular energy has also been investigated computationally. Yet, these calculations require a lot of expensive computer resources. The purpose of this project is to apply machine learning (ML) techniques to create models from known molecular properties. Once the model is created, the molecular properties of new molecules can be predicted quickly. Feedforward Neural Network (FNN) models were trained with two different representations of the molecules. In the first model, the molecules were represented by the Coulombic force between each atom; in the second model, the molecular structure, the bonding between atoms, and the electron configuration of each atom were provided as inputs. Prediction errors of the two models were compared statistically to determine the better representation of the molecule. The FNN network was able to predict the molecular energy with low errors in both models. Though, the model with the Coulomb matrix performed better for molecules that do not contain high electronegative atoms and performed poorly for molecules with three or more fluorine atoms. The effect of fluorine (or other electronegative atoms) on the Coulomb matrix needs to be further investigated.
Probiotic biosorption as a way to remove heavy metal in seawater
Authors: Cheng Justin , Fan Hao-Chun
Published: September 2023

Industrial and feedlot water waste that contain large amounts of heavy metals can be harmful for Taiwan’s aquaculture. This problem can be solved in an environmentally-friendly way by biosorption, which is using biological materials to absorb heavy metals. In this research, we aimed to reduce the food safety issues introduced by heavy metal contamination through the use of probiotics in food-producing aquafarms. Lactobacillus rhamnosus GG (LGG) and Bifidobacterium longum (BL) were added into seawater to determine if they have an ability to uptake heavy metal ions in a natural environment. Inductively coupled plasma mass spectrometry (ICP-MS) was used to detect the ion concentrations of arsenic (As), cadmium (Cd), and mercury (Hg) before and after biosorption. Both living and dead LGG showed a great biosorption capacity towards Hg and Cd, indicating that probiotics of LGG are a potential resource for efficient biosorption. Dead BL also showed a great biosorption capacity towards Cd and Hg, but much lower than living and dead LGG. Thus, the results of our experiment support the idea of using probiotics to solve heavy metal pollution issues in aquafarms in Taiwan.
A novel approach to determine which organism best displays Gijswijt's Sequence in its genome
Authors: Chaturvedi Archit , Slijk Wendy
Published: September 2023

The genomes of organisms are filled with hidden mathematical sequences present in the sequence of the nitrogenous bases that make up DNA. Using mathematical and computational tools, many of these mathematical sequences can be deciphered from the genetic code. Gijswijt’s Sequence is a mathematical integer sequence named after Dion Gijswijt and is a self-describing sequence where each term counts the maximum number of repeated blocks of numbers in the sequence that precedes the term. Therefore, we are interested in finding the organism that best displays Gijswijt’s Sequence in its genome, or has a DNA sequence somewhere in its genome that is very similar to the integer sequence. We hypothesized that there is an organism that displays Gijswijt’s Sequence multiple times in its genome with significant matches to the input DNA sequences, and therefore, is the organism that best displays the sequence in its genome. We applied Gijswijt’s Sequence to the different permutations of the four nitrogenous bases present in DNA and using the Basic Local Alignment Search Tool (BLAST) through BioPython in the Python programming language, we concluded that the common carp best displays Gijswijt’s Sequence in its genome.
The Role of a Mask - Understanding the Performance of Deep Neural Networks to Detect, Segment, and Extract Cellular Nuclei from Microscopy Images
Authors: Dasgupta Soham , Turban Stephen
Published: September 2023

Cell segmentation is the task of identifying cell nuclei instances in fluorescence microscopy images. It plays a key role in biomedical analysis tasks like cell characterization, cancer cell identification, and gene expression measurement. There has been a recent proliferation of deep neural network-based object detection techniques for cell segmentation. However, previous literature does not suitably address the proper understanding of the different methods and the merits of the various neural architectures proposed. One key design point relates to the learning of segmentation masks and how neural methods go about detecting, segmenting, and extracting nuclei from unseen images. The goal of this paper is to benchmark the performance of representative deep learning techniques for cell nuclei segmentation using standard datasets and common evaluation criteria. We investigate whether for cell nuclei segmentation, learning the nuclei masks in parallel with boundary detection features of the image provides superior performance and significantly cleaner separation of nuclei from images. We further explore the trade-off between increased accuracy, achieved through more complex deep learning models, and the heavy requirements imposed on both computational resources and training times. We believe this paper establishes an important baseline for cell nuclei segmentation, enabling researchers to continually refine and deploy neural models for real-world clinical applications.
Hammett linear free-energy relationships in the biocatalytic hydrolysis of para-substituted nitrophenyl benzoate esters
Authors: Kocalar Selin , Zhou Catherine , Tan Jadon , Liu Alex , Chen Elliott , Salahifar Aylin , Verma Pranjal , Pemmaraju Saanvi , Njoo Edward
Published: September 2023

As the drive toward more efficient, sustainable, and affordable methods of chemical synthesis continues, the focus on biocatalysts has grown significantly. Using the Hammett linear free-energy relationship (LFER), we can gain mechanistic insight into chemical transformations such as those catalyzed by enzymes. In this study, we investigated the catalytic mechanisms of trypsin, lipase, and nattokinase by using the Hammett LFER to compare the electronic effects of various para-substitutions on ester hydrolysis. We synthesized a class of nitrophenyl benzoate esters with electron-withdrawing and electron-donating para-substituents and subjected them to enzymatic hydrolysis, from which we obtained kinetic data by spectroscopically tracking the release of 4-nitrophenol, a bright yellow compound that forms upon hydrolysis. We then used the Hammett equation to analyze kinetic trends, and further supported our study with computational modeling, through which a direct correlation between the carbonyl carbon Mulliken charge and the σ_para constant was established. These results suggest that the hydrolysis reaction, when catalyzed by either of the three enzymes, exhibited a change in the rate-determining step. We also observed relative differences in enzymatic sensitivity to substrate electronic effects and enzymatic ability to stabilize charged intermediates.
Decolorization of textile dyes by edible white rot fungi
Authors: Lin Yi-Chen , Fan Hao-Chun
Published: September 2023

Properly disposing of wastewater-containing textile dyes has long been a problem for the textile industry. An innovative method, biodegradation, can degrade certain dyes more efficiently and in a more environmentally-friendly method than the commonly used physicochemical treatments. Fungus is one of the materials capable of biodegradation without requiring further processing. In this study, we tested the edible fungi, Lentinula edodes, Pleurotus eryngii, and Pleurotus ostreatus, to see if they can used for a biodegradation of dyes. The textile dyes were applied into the suspension of these fungi for a biodegradation test, and the absorbance changes were recorded. After a reaction of one and a half hours, aniline blue dye and Congo red dye demonstrate the greatest degradation, reaching a biodegradation rate of 67.39–67.5% and 58.1–63.2%, respectively. Even the methylene blue dye that had the lowest degradation reached a biodegradation rate of 24.7–33.6%. These results show the fungi’s capability to decolorize the dyes, presenting a potential method for biodegrading textile pollution and the possibility of using natural products to reduce polluted wastewater.
Expressional correlations between SERPINA6 and pancreatic ductal adenocarcinoma-linked genes
Authors: Selver Maxwell , Tibbetts Lisa
Published: September 2023

Pancreatic ductal adenocarcinoma (PDAC) is the most common form of pancreatic cancer, with early diagnosis and treatment challenges. When any of the genes KRAS, SMAD4, TP53, and BRCA2 are heavily mutated, they correlate with PDAC progression. Cellular stress, partly regulated by the gene SERPINA6, also correlates with PDAC progression. When SERPINA6 is highly expressed, corticosteroid-binding globulin inhibits the effect of the stress hormone cortisol. We hypothesized that the expression of SERPINA6 would inversely correlate with the expression of PDAC-linked genes. Healthy pancreatic expression control data was sourced from GTEx, while mutated PDAC experimental expression data was sourced from TGCA. Eight scatterplots with p, R, and R2 values were produced via Correlation Analysis on gene profiling database GEPIA2. A lack of experimental statistical significance of the KRAS and TP53 scatterplots indicate the genes do not correlate with SERPINA6. SMAD4 scatterplots demonstrated statistical significance on both ends with a direct trend, indicating a potential correlation with SERPINA6. While the control scatterplot of BRCA2 exhibited statistical insignificance, the experimental scatterplot exhibited significance in addition to a hypothesized inverse trend. This may indicate a tumor-specific correlation between BRCA2 and SERPINA6. Further exploring the viability of this potential expressional correlation may build on lacking early diagnosis techniques and further supplement the scientific community’s interest in the mind-body stress connection.