Browse Articles

Refinement of Single Nucleotide Polymorphisms of Atopic Dermatitis related Filaggrin through R packages

Naravane et al. | Oct 12, 2022

Refinement of Single Nucleotide Polymorphisms of Atopic Dermatitis related Filaggrin through R packages

In the United States, there are currently 17.8 million affected by atopic dermatitis (AD), commonly known as eczema. It is characterized by itching and skin inflammation. AD patients are at higher risk for infections, depression, cancer, and suicide. Genetics, environment, and stress are some of the causes of the disease. With the rise of personalized medicine and the acceptance of gene-editing technologies, AD-related variations need to be identified for treatment. Genome-wide association studies (GWAS) have associated the Filaggrin (FLG) gene with AD but have not identified specific problematic single nucleotide polymorphisms (SNPs). This research aimed to refine known SNPs of FLG for gene editing technologies to establish a causal link between specific SNPs and the diseases and to target the polymorphisms. The research utilized R and its Bioconductor packages to refine data from the National Center for Biotechnology Information's (NCBI's) Variation Viewer. The algorithm filtered the dataset by coding regions and conserved domains. The algorithm also removed synonymous variations and treated non-synonymous, frameshift, and nonsense separately. The non-synonymous variations were refined and ordered by the BLOSUM62 substitution matrix. Overall, the analysis removed 96.65% of data, which was redundant or not the focus of the research and ordered the remaining relevant data by impact. The code for the project can also be repurposed as a tool for other diseases. The research can help solve GWAS's imprecise identification challenge. This research is the first step in providing the refined databases required for gene-editing treatment.

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Photometric analysis and light curve modeling of apparent transient 2020pni

Arora et al. | Oct 07, 2022

Photometric analysis and light curve modeling of apparent transient 2020pni

Supernovas are powerful explosions that result from gravitational collapse of a massive star. Using photometric analysis Arora et al. set out to investigate whether 2020pni (located in galaxy UGC 9684) was a supernova. They were ultimately able to identify 2020pni as a Type II-L supernova and determine it's distance from earth.

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Societal awareness regarding viral Hepatitis in developed and developing countries

Srivastava et al. | Oct 03, 2022

Societal awareness regarding viral Hepatitis in developed and developing countries

Many cases of viral hepatitis are easily preventable if caught early; however, a lack of public awareness regarding often leads to diagnoses near the final stages of disease when it is most lethal. Thus, we wanted to understand to what extent an individual's sex, age, education and country of residence (India or Singapore) impacts disease identification. We sent out a survey and quiz to residents in India (n = 239) and Singapore (n = 130) with questions that test their knowledge and awareness of the disease. We hypothesized that older and more educated individuals would score higher because they are more experienced, but that the Indian population will not be as knowledgeable as the Singaporean population because they do not have as many resources, such as socioeconomic access to schools and accessibility to healthcare, available to them. Additionally, we predicted that there would not be any notable differences between make and females. The results revealed that the accuracy for all groups we looked at was primarily below 50%, demonstrating a severe knowledge gap. Therefore, we concluded that if more medical professionals discussed viral hepatitis during hospital visits and in schools, patients can avoid the end stages of the disease in notable cases.

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Contrasting role of ASCC3 and ALKBH3 in determining genomic alterations in Glioblastoma Multiforme

Sriram et al. | Sep 27, 2022

Contrasting role of <i>ASCC3</i> and <i>ALKBH3</i> in determining genomic alterations in Glioblastoma Multiforme

Glioblastoma Multiforme (GBM) is the most malignant brain tumor with the highest fraction of genome alterations (FGA), manifesting poor disease-free status (DFS) and overall survival (OS). We explored The Cancer Genome Atlas (TCGA) and cBioportal public dataset- Firehose legacy GBM to study DNA repair genes Activating Signal Cointegrator 1 Complex Subunit 3 (ASCC3) and Alpha-Ketoglutarate-Dependent Dioxygenase AlkB Homolog 3 (ALKBH3). To test our hypothesis that these genes have correlations with FGA and can better determine prognosis and survival, we sorted the dataset to arrive at 254 patients. Analyzing using RStudio, both ASCC3 and ALKBH3 demonstrated hypomethylation in 82.3% and 61.8% of patients, respectively. Interestingly, low mRNA expression was observed in both these genes. We further conducted correlation tests between both methylation and mRNA expression of these genes with FGA. ASCC3 was found to be negatively correlated, while ALKBH3 was found to be positively correlated, potentially indicating contrasting dysregulation of these two genes. Prognostic analysis showed the following: ASCC3 hypomethylation is significant with DFS and high ASCC3 mRNA expression to be significant with OS, demonstrating ASCC3’s potential as disease prediction marker.

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A Crossover Study Comparing the Effect of a Processed vs. Unprocessed Diet on the Spatial Learning Ability of Zebrafish

Banga et al. | Sep 18, 2022

A Crossover Study Comparing the Effect of a Processed vs. Unprocessed Diet on the Spatial Learning Ability of Zebrafish

The authors compared the short-term effects of processed versus unprocessed food on spatial learning and survival in zebrafish, given the large public concern regarding processed foods. By randomly assigning zebrafish to a diet of brine shrimp flakes (processed) or live brine shrimp (unprocessed), the authors show while there is no immediate effect on a fish's decision process between the two diets, there are significant correlations between improved learning and stress response with the unprocessed diet.

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Effects of caffeine on muscle signals measured with sEMG signals

Park et al. | Jun 20, 2022

Effects of caffeine on muscle signals measured with sEMG signals

Here, the authors used surface electromyography to measure the effects of caffeine intake on the resting activity of muscles. They found a significant increase in the measured amplitude suggesting that caffeine intake increased the number of activated muscle fibers during rest. While previous research has focused on caffeine's effect on the contraction signals of muscles, this research suggests that its effects extend to even when a muscle is at rest.

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A new therapy against MDR bacteria by in silico virtual screening of Pseudomonas aeruginosa LpxC inhibitors

Liu et al. | Apr 27, 2022

A new therapy against MDR bacteria by <em>in silico</em> virtual screening of <em>Pseudomonas aeruginosa</em> LpxC inhibitors

Here, seeking to address the growing threat of multidrug-resistant bacteria (MDR). the authors used in silico virtual screening to target MDR Pseudomonas aeruginosa. They considered a key protein in its biosynthesis and virtually screened 20,000 candidates and 30 derivatives of brequinar. In the end, they identified a possible candidate with the highest degree of potential to inhibit the pathogen's lipid A synthesis.

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Comparing Measurements of Sun-Earth Distance: Shadow Method and Two Pinhole Method Variations

Rajakumar et al. | Feb 21, 2022

Comparing Measurements of Sun-Earth Distance: Shadow Method and Two Pinhole Method Variations

This study compares three methods regarding their accuracy in calculating the distance between the Earth and the Sun. The hypothesis presented was that the shadow method would have the greatest mean accuracy, followed by the tube pinhole method, and finally the plate pinhole method. The results validate the hypothesis; however, further investigation would be helpful in determining effective mitigation of each method’s limitations and the effectiveness of each method in determining the distance of other light-emitting objects distant from the Earth.

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Firearm-purchase laws that limit the number of guns on the market reduce gun homicides in the South Side of Chicago

Krishnan et al. | Jan 24, 2022

Firearm-purchase laws that limit the number of guns on the market reduce gun homicides in the South Side of Chicago

Gun violence has been a serious issue in the South Side of Chicago for a long time. To intervene, regulators have passed legislation they hoped to curb -if not completely eradicate- the issue. However, there is little analysis done on how effective the various laws have been at reducing gun violence. Here the authors explore the association between firearm purchase laws passed between 1993-2018 and the incidence of gun homicide in Chicago's South Side. Their analysis suggests that some laws have been more effective than others, while some might have exacerbated the issue. However, they do not consider other contributing factors, which makes it difficult to prove causation without further investigation.

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A study on the stretching behavior of rubber bands

Davuluri et al. | Jan 18, 2022

A study on the stretching behavior of rubber bands

Here, the authors considered the stretching behavior of rubber bands by exposing the rubber bands to increasing loads and measuring their stretch response. They found that a linear stretch response was observed for intermediate loading steps, but this behavior was lost at lower or higher loads, deviating from Hooke's Law. The authors suggest that studies such as these can be used to evaluate other visco-elastic structures.

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