University of Toronto Journal of Undergraduate Life Sciences最新文献_第3页

Visualization of Layers Within a Convolutional Neural Network Using Gradient Activation Maps 使用梯度激活图的卷积神经网络层可视化

IF 0.2

University of Toronto Journal of Undergraduate Life Sciences Pub Date : 2020-12-31 DOI: 10.33137/juls.v14i1.35833

D. McAllister, Mauro Mendez, Ariana Bermúdez, P. Tyrrell

{"title":"Visualization of Layers Within a Convolutional Neural Network Using Gradient Activation Maps","authors":"D. McAllister, Mauro Mendez, Ariana Bermúdez, P. Tyrrell","doi":"10.33137/juls.v14i1.35833","DOIUrl":"https://doi.org/10.33137/juls.v14i1.35833","url":null,"abstract":"Introduction: Convolutional neural networks (CNNs) are machine learning tools that have great potential in the field of medical imaging. However, it is often regarded as a “black box” as the process that is used by the machine to acquire a result is not transparent. It would be valuable to find a method to be able to understand how the machine comes to its decision. Therefore, the purpose of this study is to examine how effective gradient-weighted class activation mapping (grad-CAM) visualizations are for certain layers in a CNN-based dental x-ray artifact prediction model. \u0000Methods: To tackle this project, Python code using PyTorch trained a CNN to classify dental plates as unusable or usable depending on the presence of artifacts. Furthermore, Python using PyTorch was also used to overlay grad-CAM visualizations on the given input images for various layers within the model. One image with seventeen different overlays of artifacts was used in this study. \u0000Results: In earlier layers, the model appeared to focus on general features such as lines and edges of the teeth, while in later layers, the model was more interested in detailed aspects of the image. All images that contained artifacts resulted in the model focusing on more detailed areas of the image rather than the artifacts themselves. Whereas the images without artifacts resulted in the model focusing on the visualization of areas that surrounded the teeth. \u0000Discussion and Conclusion: As subsequent layers examined more detailed aspects of the image as shown by the grad-CAM visualizations, they provided better insight into how the model processes information when it is making its classifications. Since all the images with artifacts showed similar trends in the visualizations of the various layers, it provides evidence to suggest that the location and size of the artifact does not affect the model’s pattern recognition and image classification.","PeriodicalId":40102,"journal":{"name":"University of Toronto Journal of Undergraduate Life Sciences","volume":" ","pages":""},"PeriodicalIF":0.2,"publicationDate":"2020-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46802785","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 2

Polycystic Ovary Syndrome: Dietary Approaches to Counteract Insulin Resistance 多囊卵巢综合征：对抗胰岛素抵抗的饮食方法

IF 0.2

University of Toronto Journal of Undergraduate Life Sciences Pub Date : 2020-12-30 DOI: 10.33137/juls.v14i1.35925

I. Das

{"title":"Polycystic Ovary Syndrome: Dietary Approaches to Counteract Insulin Resistance","authors":"I. Das","doi":"10.33137/juls.v14i1.35925","DOIUrl":"https://doi.org/10.33137/juls.v14i1.35925","url":null,"abstract":"Background: Polycystic ovary syndrome (PCOS) is a prevalent hormonal disorder connected to ovulatory infertility and recent research indicates that different diets alter the risk of developing PCOS. Insulin resistance (IR) is one of the key pathologies which classifies PCOS. Understanding the etiology leading to IR in PCOS patients and the disorders associated with IR can allow for a therapeutic measure to be put in place to counteract the etiology and even reduce the risk of developing the disorder. Objective: The objective of this review is to identify the key factors that lead to IR so that diet and other lifestyle aspects can be used to counteract PCOS Symptoms.Design: A total of 679 studies were taken into consideration for this review, however, I performed a literature review of 75 primary papers. Data and findings from these studies were used to gain a better understanding of the dietary etiology of IR in PCOS, and this information can be used to describe a specific diet to counteract its etiology.Results: Many symptoms and disorders in the biological pathway of PCOS is associated with IR. Clinical studies have established that an increase in carbohydrates, low-density lipoproteins, and triglycerides is associated with IR in PCOS patients. Similar studies have found that a decrease in dietary proteins (especially branched chain amino acid intake), lactate, phosphatidylcholine, high-density lipoproteins, and long-chain fatty acids are also associated with PCOS patients. The drug metformin has also been associated with ameliorating many of the negative impacts imposed by IR in PCOS patients. Addressing these factors and changing diet and lifestyle (such as increased exercise) can help reduce the IR-related effects in PCOS patients.","PeriodicalId":40102,"journal":{"name":"University of Toronto Journal of Undergraduate Life Sciences","volume":" ","pages":""},"PeriodicalIF":0.2,"publicationDate":"2020-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44724864","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Students’ Perspectives on Undergraduate Research: Obstacles, Experiences, and Tips for a Refined Young Scientist 学生对本科研究的看法:一个优雅的青年科学家的障碍、经验和建议

IF 0.2

University of Toronto Journal of Undergraduate Life Sciences Pub Date : 2020-12-30 DOI: 10.33137/juls.v14i1.35924

Kritleen K. Bawa, Layan A Elfaki, Kevin Tang

引用次数: 0

Ketene and Ammonia Forming Acetamide in the Interstellar Medium 烯酮和氨在星际介质中形成乙酰胺

IF 0.2

University of Toronto Journal of Undergraduate Life Sciences Pub Date : 2020-12-14 DOI: 10.33137/juls.v14i1.35210

Akash Kothari, Ling-Zhi Zhu, Jon Babi, Natalie J. Galant, A. Rágyanszki, I. Csizmadia

{"title":"Ketene and Ammonia Forming Acetamide in the Interstellar Medium","authors":"Akash Kothari, Ling-Zhi Zhu, Jon Babi, Natalie J. Galant, A. Rágyanszki, I. Csizmadia","doi":"10.33137/juls.v14i1.35210","DOIUrl":"https://doi.org/10.33137/juls.v14i1.35210","url":null,"abstract":"Background: Peptide bonds are among the fundamental building blocks of life, polymerizing amino acids to form proteins that make up the structural components of living cells and regulate biochemical processes. The detection of glycine by NASA in comet Wild 2 in 2009 suggests the possibility of the formation of biomolecules in extraterrestrial environments through the interstellar medium. Detected in the dense molecular cloud Sagittarius B2, acetamide is the largest molecule containing a peptide bond and is hypothesized to be the precursor to all amino acids; as such, viability of its formation is of important biological relevance. \u0000Methods: Under a proposed mechanism of ammonia and ketene reactants, which have also been detected in dense molecular clouds in the ISM, the reaction pathway for the formation of acetamide was modelled using quantum chemical calculations in Gaussian16, using Austin-Frisch-Petersson functional with dispersion density functional theory at a 6-31G(d) basis set level of theory to optimize geometries and determine the thermodynamic properties for the reaction. Stability of the reactants, transition states, and products were examined to establish a reasonable mechanism. \u0000Conclusion: Product formation of acetamide was found to be highly exergonic and exothermic with a low energy barrier, suggesting a mechanism that is viable in the extreme density and temperature conditions found in ISM.","PeriodicalId":40102,"journal":{"name":"University of Toronto Journal of Undergraduate Life Sciences","volume":" ","pages":""},"PeriodicalIF":0.2,"publicationDate":"2020-12-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48105827","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 3

Quantum Chemical Study of the Formation of Urea in Interstellar Medium 星际介质中尿素生成的量子化学研究

IF 0.2

University of Toronto Journal of Undergraduate Life Sciences Pub Date : 2020-12-14 DOI: 10.33137/juls.v14i1.35211

Ling-Zhi Zhu, Akash Kothari, Jon Babi, Natalie J. Galant, A. Rágyanszki, I. Csizmadia

{"title":"Quantum Chemical Study of the Formation of Urea in Interstellar Medium","authors":"Ling-Zhi Zhu, Akash Kothari, Jon Babi, Natalie J. Galant, A. Rágyanszki, I. Csizmadia","doi":"10.33137/juls.v14i1.35211","DOIUrl":"https://doi.org/10.33137/juls.v14i1.35211","url":null,"abstract":"Background: Many observational studies have found the presence of organic molecules in interstellar medium (ISM) via spectroscopy. NH2CONH2 (urea) was first detected in ISM in 2014. Containing two NH2 groups, urea is an important biological molecule in metabolism as a carrier for waste nitrogen. The discovery of urea in ISM suggests the possibility of the formation of other biomolecules which contain peptide bonds, such as proteins. This supports the origin of life theory proposing that these biomolecules were initially formed in space and later arrived to Earth. \u0000Methods: This study investigates two possible reaction pathways for the formation of protonated urea (ureaH+) in dense molecular clouds via molecules previously observed in the ISM, formamide (HCONH2) and protonated hydroxylamine (NH2OH2+). The thermodynamics and optimized geometries were calculated for the final steps of the formation of ureaH+ using Gaussian16 at the APFD/6-31G(d,p) level of theory and a transition state was confirmed. \u0000Results: The overall mechanism, as well as the studied proton rearrangement of an intermediate to ureaH+, were found to be exothermic and exergonic processes. \u0000Conclusion: From the calculations, the conditions of ISM provide an adequate environment for the formation of ureaH+ and urea.","PeriodicalId":40102,"journal":{"name":"University of Toronto Journal of Undergraduate Life Sciences","volume":"1 1","pages":""},"PeriodicalIF":0.2,"publicationDate":"2020-12-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41913906","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 2