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Using explainable artificial intelligence to identify patient-specific breast cancer subtypes

Suresh et al. | Jan 12, 2024

Using explainable artificial intelligence to identify patient-specific breast cancer subtypes

Breast cancer is the most common cancer in women, with approximately 300,000 diagnosed with breast cancer in 2023. It ranks second in cancer-related deaths for women, after lung cancer with nearly 50,000 deaths. Scientists have identified important genetic mutations in genes like BRCA1 and BRCA2 that lead to the development of breast cancer, but previous studies were limited as they focused on specific populations. To overcome limitations, diverse populations and powerful statistical methods like genome-wide association studies and whole-genome sequencing are needed. Explainable artificial intelligence (XAI) can be used in oncology and breast cancer research to overcome these limitations of specificity as it can analyze datasets of diagnosed patients by providing interpretable explanations for identified patterns and predictions. This project aims to achieve technological and medicinal goals by using advanced algorithms to identify breast cancer subtypes for faster diagnoses. Multiple methods were utilized to develop an efficient algorithm. We hypothesized that an XAI approach would be best as it can assign scores to genes, specifically with a 90% success rate. To test that, we ran multiple trials utilizing XAI methods through the identification of class-specific and patient-specific key genes. We found that the study demonstrated a pipeline that combines multiple XAI techniques to identify potential biomarker genes for breast cancer with a 95% success rate.

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Effects of various alkaline carbonic solutions on the growth of the freshwater algae Chlorophyceae

Jani et al. | Aug 11, 2023

Effects of various alkaline carbonic solutions on the growth of the freshwater algae Chlorophyceae
Image credit: Jordan Whitfield

Modern day fossil fuels are prone to polluting our environment, which can provide major habitat loss to many animals in our ecosystems. Algae-based biofuels have become an increasingly popular alternative to fossil fuels because of their sustainability, effectiveness, and environmentally-friendly nature. To encourage algae growth and solidify its role as an emerging biofuel, we tested basic (in terms of pH) solutions on pond water to determine which solution is most efficient in inducing the growth of algae.

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Development and Implementation of Enzymatic and Volatile Compound-based Approaches for Instantaneous Detection of Pathogenic Staphylococcus aureus

Nori et al. | Feb 20, 2021

Development and Implementation of Enzymatic and Volatile Compound-based Approaches for Instantaneous Detection of Pathogenic <i>Staphylococcus aureus</i>

Staphylococcus aureus (S. aureus) has a mortality rate of up to 30% in developing countries. The purpose of this experiment was to determine if enzymatic and volatile compound-based approaches would perform more quickly in comparison to existing S. aureus diagnostic methods and to evaluate these novel methods on accuracy. Ultimately, this device provided results in less than 30 seconds, which is much quicker than existing methods that take anywhere from 10 minutes to 48 hours based on approach. Statistical analysis of accuracy provides preliminary confirmation that the device based on enzymatic and volatile compound-based approaches can be an accurate and time-efficient tool to detect pathogenic S. aureus.

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Investigating the Role of the Novel ESCRT-III Recruitment Factor CCDC11 in HIV Budding: A Potential Target for Antiviral Therapy

Takemaru et al. | Feb 24, 2020

Investigating the Role of the Novel ESCRT-III Recruitment Factor CCDC11 in HIV Budding: A Potential Target for Antiviral Therapy

Acquired immunodeficiency syndrome (AIDS) is a life-threatening condition caused by the human immunodeficiency virus (HIV). In this work, Takemaru et al explored the role of Coiled-Coil Domain-Containing 11 (CCDC11) in HIV-1 budding. Their results suggest that CCDC11 is critical for efficient HIV-1 budding, potentially indicating CCDC11 a viable target for antiviral therapeutics without major side effects.

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Changes for Development of Al2O3 Coated PVA (Polyvinyl Alcohol) Composite Nonwoven Separator For Improving Thermal and Electrochemical Properties

Kim et al. | Oct 16, 2019

Changes for Development of Al2O3 Coated PVA (Polyvinyl Alcohol) Composite Nonwoven Separator For Improving Thermal and Electrochemical Properties

Lithium-ion batteries, a breakthrough in chemistry that enabled the electronic revolution we live today have become an essential part of our day-to-day life. A phone battery running out after a heavy day of use with limited opportunities for recharging is a well-known and resented experience by almost everyone. How then can we make batteries more efficient? This paper proposes the use of a different type of separator, that improves the charging and discharging capacities of lithium ions compared to the classical separator. This and similar attempts to improve Lithium-ion battery function could facilitate the development of higher-performance batteries that work longer and withstand harsher use.

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3D Printed Polymer Scaffolds for Bone Tissue Regeneration

Jayatissa et al. | Apr 26, 2019

3D Printed Polymer Scaffolds for Bone Tissue Regeneration

Scientists are always on the quest to improve the body's healing abilities and broken bones are no exception. In this article, the authors investigate properties of 3D-printed biocompatible polymers used to improve bone healing. With such efforts, we can hope to, one day, improve bone scaffolding materials in ways that make the natural healing processes more efficient, reducing the time needed for recovery from bone fractures.

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Phages Can Be More Effective and Specific Than Antibiotics in Combating Bacteria

Wu et al. | Feb 17, 2019

Phages Can Be More Effective and Specific Than Antibiotics in Combating Bacteria

Phage therapy has been suggested as an alternative to antibiotics because bacteria resistant to antibiotics may still be susceptible to phages. However, phages may have limited effectiveness in combating bacteria since bacteria possess several antiviral defense mechanisms and can quickly develop resistance to phages. In this study, Wu and Pinta compare the effectiveness and specificity of antibiotics and phages in combating bacteria. They found that T4 phages are more specific and effective in fighting or inhibiting both antibiotic-resistant and sensitive bacteria than antibiotics, suggesting that phage therapy can be developed as an efficient tool to combat antibiotic-resistant bacteria.

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Determining the Effects of Fibroblast Growth Factor 2 on the Regenerative Abilities of Echinometra lucunter Sea Urchins

Kisling et al. | Feb 12, 2019

Determining the Effects of Fibroblast Growth Factor 2 on the Regenerative Abilities of Echinometra lucunter Sea Urchins

As humans, not all our body organs can adequately regenerate after injury, an ability that declines with age. In some species, however, regeneration is a hallmark response that can occur limitless numbers of time throughout the life of an organism. Understanding how such species can regenerate so efficiently is of central importance to regenerative medicine. Sea urchins, unlike humans, can regenerate their spinal tissue after injury. Here the authors study the effect of a growth factor, FGF2, on sea urchin regeneration but find no conclusive evidence for a pro-regenerative effect after spinal tissue injury.

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The Effect of Radiant Energy on Radish Seed Germination

Simon et al. | Jul 06, 2018

The Effect of Radiant Energy on Radish Seed Germination

Simon and colleagues test how exposure to microwaves affect radish seed germination, either microwaving seeds for ninety seconds or four minutes prior to planting. Surprisingly, the authors found that seeds microwaved for four minutes exhibited 150% increased germination as compared to controls. The authors hypothesize that breakdown of the radish seed coat when exposed to heat may allow seedlings to sprout more efficiently.

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A Simple Printing Solution to Aid Deficit Reduction

Mirchandani et al. | Mar 09, 2014

A Simple Printing Solution to Aid Deficit Reduction

The printing-related expenditure that is budgeted in 2014 for U.S. Federal agencies is $1.8 billion. A sample of five publically available documents produced by various federal agencies is analyzed and the cost savings arising from a change in font type are estimated. The analysis predicts that the Government’s annual savings by switching to Garamond are likely to be about $234 million with worst-case savings of $62 million and best-case savings of $394 million. Indirect benefits arising from a less detrimental impact on the environment due to lower ink production and disposal volumes are not included in these estimates. Times New Roman is not as efficient as Garamond, and the third federally-recommended font, Century Gothic, is actually worse on average than the fonts used in the sample documents.

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