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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Gradient boosting with temporal feature extraction for modeling keystroke log data

Barretto et al. | Oct 04, 2024

Gradient boosting with temporal feature extraction for modeling keystroke log data
Image credit: Barretto and Barretto 2024.

Although there has been great progress in the field of Natural language processing (NLP) over the last few years, particularly with the development of attention-based models, less research has contributed towards modeling keystroke log data. State of the art methods handle textual data directly and while this has produced excellent results, the time complexity and resource usage are quite high for such methods. Additionally, these methods fail to incorporate the actual writing process when assessing text and instead solely focus on the content. Therefore, we proposed a framework for modeling textual data using keystroke-based features. Such methods pay attention to how a document or response was written, rather than the final text that was produced. These features are vastly different from the kind of features extracted from raw text but reveal information that is otherwise hidden. We hypothesized that pairing efficient machine learning techniques with keystroke log information should produce results comparable to transformer techniques, models which pay more or less attention to the different components of a text sequence in a far quicker time. Transformer-based methods dominate the field of NLP currently due to the strong understanding they display of natural language. We showed that models trained on keystroke log data are capable of effectively evaluating the quality of writing and do it in a significantly shorter amount of time compared to traditional methods. This is significant as it provides a necessary fast and cheap alternative to increasingly larger and slower LLMs.

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Color photometry and light curve modeling of apparent transient 2023jri

Favretto et al. | Aug 13, 2024

Color photometry and light curve modeling of apparent transient 2023jri

Observing transients like supernovae, which have short-lived brightness variations, helps astronomers understand cosmic phenomena. This study analyzed transient 2023jri, hypothesizing it was a Type IIb supernova. By collecting and analyzing data over four weeks, including light and color curves, they confirmed its classification and provided additional insights into this less-studied supernova type.

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Suppress that algae: Mitigating the effects of harmful algal blooms through preemptive detection & suppression

Natarajan et al. | Jul 17, 2023

Suppress that algae: Mitigating the effects of harmful algal blooms through preemptive detection & suppression
Image credit: Sharanya Natarajan

A bottleneck in deleting algal blooms is that current data section is manual and is reactionary to an existing algal bloom. These authors made a custom-designed Seek and Destroy Algal Mitigation System (SDAMS) that detects harmful algal blooms at earlier time points with astonishing accuracy, and can instantaneously suppress the pre-bloom algal population.

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The Cohesiveness of the Oscillating Belousov-Zhabotinsky Reaction

Gottlieb et al. | Dec 18, 2018

The Cohesiveness of the Oscillating Belousov-Zhabotinsky Reaction

In this study the author undertakes a careful characterization of a special type of chemical reaction, called an oscillating Belousov-Zhabotinsky (or B-Z) reaction, which has a number of existing applications in biomedical engineering as well as the potential to be useful in future developments in other fields of science and engineering. Specifically, she uses experimental measurements in combination with computational analysis to investigate whether the reaction is cohesive – that is, whether the oscillations between chemical states will remain consistent or change over time as the reaction progresses. Her results indicate that the reaction is not cohesive, providing an important foundation for the development of future technologies using B-Z reactions.

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