AIMS Biophysics最新文献_第6页

Feature selection and classification approaches in gene expression of breast cancer 乳腺癌基因表达的特征选择与分类方法

IF 1.5

AIMS Biophysics Pub Date : 2021-01-01 DOI: 10.3934/biophy.2021029

Sarada Ghosh, Guruprasad Samanta, M. de La Sen

{"title":"Feature selection and classification approaches in gene expression of breast cancer","authors":"Sarada Ghosh, Guruprasad Samanta, M. de La Sen","doi":"10.3934/biophy.2021029","DOIUrl":"https://doi.org/10.3934/biophy.2021029","url":null,"abstract":"DNA microarray technology with biological data-set can monitor the expression levels of thousands of genes simultaneously. Microarray data analysis is important in phenotype classification of diseases. In this work, the computational part basically predicts the tendency towards mortality using different classification techniques by identifying features from the high dimensional dataset. We have analyzed the breast cancer transcriptional genomic data of 1554 transcripts captured over from 272 samples. This work presents effective methods for gene classification using Logistic Regression (LR), Random Forest (RF), Decision Tree (DT) and constructs a classifier with an upgraded rate of accuracy than all features together. The performance of these underlying methods are also compared with dimension reduction method, namely, Principal Component Analysis (PCA). The methods of feature reduction with RF, LR and decision tree (DT) provide better performance than PCA. It is observed that both techniques LR and RF identify TYMP, ERS1, C-MYB and TUBA1a genes. But some features corresponding to the genes such as ARID4B, DNMT3A, TOX3, RGS17 and PNLIP are uniquely pointed out by LR method which are leading to a significant role in breast cancer. The simulation is based on R-software.","PeriodicalId":7529,"journal":{"name":"AIMS Biophysics","volume":"1 1","pages":""},"PeriodicalIF":1.5,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70185184","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: 0

A basic introduction to single particles cryo-electron microscopy 单粒子低温电子显微镜的基本介绍

IF 1.5

AIMS Biophysics Pub Date : 2021-01-01 DOI: 10.3934/biophy.2022002

Vittoria Raimondi, A. Grinzato

{"title":"A basic introduction to single particles cryo-electron microscopy","authors":"Vittoria Raimondi, A. Grinzato","doi":"10.3934/biophy.2022002","DOIUrl":"https://doi.org/10.3934/biophy.2022002","url":null,"abstract":"In the last years, cryogenic-electron microscopy (cryo-EM) underwent the most impressive improvement compared to other techniques used in structural biology, such as X-ray crystallography and NMR. Electron microscopy was invented nearly one century ago but, up to the beginning of the last decades, the 3D maps produced through this technique were poorly detailed, justifying the term “blobbology” to appeal to cryo-EM. Recently, thanks to a new generation of microscopes and detectors, more efficient algorithms, and easier access to computational power, single particles cryo-EM can routinely produce 3D structures at resolutions comparable to those obtained with X-ray crystallography. However, unlike X-ray crystallography, which needs crystallized proteins, cryo-EM exploits purified samples in solution, allowing the study of proteins and protein complexes that are hard or even impossible to crystallize. For these reasons, single-particle cryo-EM is often the first choice of structural biologists today. Nevertheless, before starting a cryo-EM experiment, many drawbacks and limitations must be considered. Moreover, in practice, the process between the purified sample and the final structure could be trickier than initially expected. Based on these observations, this review aims to offer an overview of the principal technical aspects and setups to be considered while planning and performing a cryo-EM experiment.","PeriodicalId":7529,"journal":{"name":"AIMS Biophysics","volume":"152 1","pages":""},"PeriodicalIF":1.5,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70184737","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

2D vs 3D tracking in bacterial motility analysis 细菌运动分析中的二维与三维跟踪

IF 1.5

AIMS Biophysics Pub Date : 2021-01-01 DOI: 10.3934/biophy.2021030

J. Acres, J. Nadeau

引用次数: 3

Chest X-Ray image and pathological data based artificial intelligence enabled dual diagnostic method for multi-stage classification of COVID-19 patients 基于胸部x线图像和病理数据的人工智能实现了COVID-19患者多阶段分类的双重诊断方法

IF 1.5

AIMS Biophysics Pub Date : 2021-01-01 DOI: 10.3934/biophy.2021028

Swarnava Biswas, Debajit Sen, D. Bhatia, P. Phukan, M. Mukherjee

{"title":"Chest X-Ray image and pathological data based artificial intelligence enabled dual diagnostic method for multi-stage classification of COVID-19 patients","authors":"Swarnava Biswas, Debajit Sen, D. Bhatia, P. Phukan, M. Mukherjee","doi":"10.3934/biophy.2021028","DOIUrl":"https://doi.org/10.3934/biophy.2021028","url":null,"abstract":"The use of Artificial Intelligence (AI) in combination with Internet of Things (IoT) drastically reduces the need to test the COVID samples manually, saving not only time but money and ultimately lives. In this paper, the authors have proposed a novel methodology to identify the COVID-19 patients with an annotated stage to enable the medical staff to manually activate a geo-fence around the subject thus ensuring early detection and isolation. The use of radiography images with pathology data used for COVID-19 identification forms the first-ever contribution by any research group globally. The novelty lies in the correct stage classification of COVID-19 subjects as well. The present analysis would bring this AI Model on the edge to make the facility an IoT-enabled unit. The developed system has been compared and extensively verified thoroughly with those of clinical observations. The significance of radiography imaging for detecting and identification of COVID-19 subjects with severity score tag for stage classification is mathematically established. In a Nutshell, this entire algorithmic workflow can be used not only for predictive analytics but also for prescriptive analytics to complete the entire pipeline from the diagnostic viewpoint of a doctor. As a matter of fact, the authors have used a supervised based learning approach aided by a multiple hypothesis based decision fusion based technique to increase the overall system's accuracy and prediction. The end to end value chain has been put under an IoT based ecosystem to leverage the combined power of AI and IoT to not only detect but also to isolate the coronavirus affected individuals. To emphasize further, the developed AI model predicts the respective categories of a coronavirus affected patients and the IoT system helps the point of care facilities to isolate and prescribe the need of hospitalization for the COVID patients.","PeriodicalId":7529,"journal":{"name":"AIMS Biophysics","volume":"25 1","pages":""},"PeriodicalIF":1.5,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70185146","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

2021-end editorial: achievements, thanks, perspectives 2021年底社论:成就、感谢、展望

IF 1.5

AIMS Biophysics Pub Date : 2021-01-01 DOI: 10.3934/biophy.2022001

C. Bianca

引用次数: 0

Enzyme-instructed self-assembly of peptides: Process, dynamics, nanostructures, and biomedical applications 酶指导的肽自组装：过程、动力学、纳米结构和生物医学应用

IF 1.5

AIMS Biophysics Pub Date : 2020-09-26 DOI: 10.3934/BIOPHY.2020028

Y. Chen, B. Liu, Lei Guo, Zhong-Liang Xiong, Gang We

{"title":"Enzyme-instructed self-assembly of peptides: Process, dynamics, nanostructures, and biomedical applications","authors":"Y. Chen, B. Liu, Lei Guo, Zhong-Liang Xiong, Gang We","doi":"10.3934/BIOPHY.2020028","DOIUrl":"https://doi.org/10.3934/BIOPHY.2020028","url":null,"abstract":"Biomolecular self-assembly provides a potential way for the design and synthesis of functional biomaterials with uniform structure and unique properties, in which the self-assembly of peptide molecules is especially important ascribed to the controllable structural design and functional tailoring of peptide motifs. The self-assembly of peptides can be instructed by internal and external physical, chemical, and biological stimulations. Compared to both physical and chemical stimulations including light/thermal treatment, pH/ionic strength adjustment, and others, the biological mediation with enzymes exhibited great advantages due to its high bioactivity, excellent biocompatibility, high specificity, and in vivo reaction. Herein we summarize the advance in the enzyme-instructed peptide self-assembly for biomedical applications. For this aim, we introduce and discuss the self-assembly of peptide that controlled by both kinetics and dynamics, and then demonstrate the enzyme-induced preparation of peptide nanostructures such as nanofibers, nanotubes, vesicles, networks, and hydrogels. Finally, the biomedical applications of enzyme-induced self-assembled peptide nanomaterials for cancer diagnostics, cancer therapy, bioelectronic devices, and biosensors are presented. It is expected this work will inspire more studies on the using of bioactive enzymes for triggering the self-assembly of peptides to create various novel bionanomaterials, which could extend this interesting research field to others such as tissue engineering, biocatalysis, energy storage, and environmental science.","PeriodicalId":7529,"journal":{"name":"AIMS Biophysics","volume":" ","pages":""},"PeriodicalIF":1.5,"publicationDate":"2020-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42459248","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: 0

Thermodynamic, kinetic and docking studies of some unsaturated fatty acids-quercetin derivatives as inhibitors of mushroom tyrosinase 一些不饱和脂肪酸-槲皮素衍生物作为蘑菇酪氨酸酶抑制剂的热力学、动力学和对接研究

IF 1.5

AIMS Biophysics Pub Date : 2020-09-01 DOI: 10.3934/biophy.2020027

Morteza Vaezi, G. Behbehani, A. Farasat, N. Gheibi, Cellular

{"title":"Thermodynamic, kinetic and docking studies of some unsaturated fatty acids-quercetin derivatives as inhibitors of mushroom tyrosinase","authors":"Morteza Vaezi, G. Behbehani, A. Farasat, N. Gheibi, Cellular","doi":"10.3934/biophy.2020027","DOIUrl":"https://doi.org/10.3934/biophy.2020027","url":null,"abstract":"Inhibition of activity and stability structure of mushroom tyrosinase (MT) is highly important, since it is a key enzyme of melanogenesis playing various roles in organisms. In this study, thermodynamic stability and diphenolase activities were investigated in the presence of quercetin-7-linoleate (ligand I) and quercetin-7-oleate (ligand II) on mushroom tyrosinase by experimental and computational methods. Kinetic analyses showed that the inhibition mechanism of these ligands is reversible and competitive manner. The inhibition constants values (KiI = 0.31 and KiII = 0.43 mM) and the half maximal inhibitory concentration (IC50 = 0.58 and 0.71 mM) were determined for ligand I and ligand II respectively. Thermal denaturation for the sole and modified enzyme were performed by using fluorescence spectroscopy to obtain the thermodynamic parameters of denaturation. Type of interactions and orientation of ligands were determined by molecular docking simulations. The binding affinities of the MT–ligand complexes during docking were calculated. In the computational studies performed using the MT (PDBID: 2Y9X) from which tropolone was removed, we showed that the ligands occupied different pockets in MT other than the active site. The best binding energies with values of −9 and −7.9 kcal/mol were calculated and the MolDock scores of the best poses with the lowest root mean square deviation (RMSD) were obtained as −172.70 and −165.75 kcal/mol for complexes of MT–ligand I and MT–ligand II, respectively. Computational simulations and experimental analysis demonstrated that the ligands increased the mushroom tyrosinase stability by reducing the activity of enzyme. In this regard, ligand I showed the potent inhibitory and played an important role in enzyme stability.","PeriodicalId":7529,"journal":{"name":"AIMS Biophysics","volume":" ","pages":""},"PeriodicalIF":1.5,"publicationDate":"2020-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45183881","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: 7

Nanoparticle-based delivery platforms for mRNA vaccine development 用于mRNA疫苗开发的基于纳米粒子的递送平台

IF 1.5

AIMS Biophysics Pub Date : 2020-08-16 DOI: 10.3934/biophy.2020023

S. Okay, Ö. Özcan, M. Karahan

{"title":"Nanoparticle-based delivery platforms for mRNA vaccine development","authors":"S. Okay, Ö. Özcan, M. Karahan","doi":"10.3934/biophy.2020023","DOIUrl":"https://doi.org/10.3934/biophy.2020023","url":null,"abstract":"Conventional vaccines have saved millions of lives, and new vaccines have also been developed; however, an urgent need for an efficient vaccine against SARS-CoV-2 showed us that vaccine development technologies should be improved more to obtain prophylactic agents rapidly during pandemic diseases. One of the next-generation vaccine technologies is utilization of mRNA molecules encoding antigens. The mRNA vaccines offer many advantages compared to conventional and other subunit vaccines. For instance, mRNA vaccines are relatively safe since they do not cause disease and mRNA does not integrate into the genome. mRNA vaccines also provide diverse types of immune responses resulting in the activation of CD4+ and CD8+ T cells. However, utilization of mRNA molecules also has some drawbacks such as degradation by ubiquitous nucleases in vivo. Nanoparticles (NPs) are delivery platforms that carry the desired molecule, a drug or a vaccine agent, to the target cell such as antigen presenting cells in the case of vaccine development. NP platforms also protect mRNA molecules from the degradation by nucleases. Therefore, efficient mRNA vaccines can be obtained via utilization of NPs in the formulation. Although lipid-based NPs are widely preferred in vaccine development due to the nature of cell membrane, there are various types of other NPs used in vaccine formulations, such as virus-like particles (VLPs), polymers, polypeptides, dendrimers or gold NPs. Improvements in the NP delivery technologies will contribute to the development of mRNA vaccines with higher efficiency.","PeriodicalId":7529,"journal":{"name":"AIMS Biophysics","volume":" ","pages":""},"PeriodicalIF":1.5,"publicationDate":"2020-08-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48959979","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: 11

Effects of treated water with neodymium magnets (NdFeB) on growth characteristics of pepper (Capsicum annuum) 钕铁硼处理水对辣椒生长特性的影响

IF 1.5

AIMS Biophysics Pub Date : 2020-07-07 DOI: 10.3934/biophy.2020021

Etimad M. Alattar, Khitam Alwasife, Eqbal Radwan

{"title":"Effects of treated water with neodymium magnets (NdFeB) on growth characteristics of pepper (Capsicum annuum)","authors":"Etimad M. Alattar, Khitam Alwasife, Eqbal Radwan","doi":"10.3934/biophy.2020021","DOIUrl":"https://doi.org/10.3934/biophy.2020021","url":null,"abstract":"This study was conducted to investigate the effect of magnetic water treatment on growth characteristics of pepper (Capsicum annuum) plants. One week old pepper plants were selected and divided into four groups in a complete randomized design. In our study, we took normal tap water and divided it into four parts. The first group received given non-magnetically treated water (as a control), while the remaining groups received magnetized water at 3, 6, and 9 magnets, respectively. Four pipes and 18 permanent magnets with a flux density of 70 mT were used for this system. The results of the current study showed that magnetized water caused significant increases in all studied parameters, except plant length and dry weight, when compared to non-magnetized water. The results revealed that magnetizing water with 6 magnets was effective than others in increasing the number of fruits and leaves per plant, whereas magnetizing water with 9 magnets was effective than others in increasing the fresh weight of produces fruits. The impact of magnetic water treatment depends on the number of magnets used to magnetizing water. It appears that the utilization of magnetically treated water can lead to improving the quantity and quality of pepper fruits. Therefore, applying magnetized water could be one of the most promising ways to enhance agricultural production in an environmentally friendly way.","PeriodicalId":7529,"journal":{"name":"AIMS Biophysics","volume":" ","pages":""},"PeriodicalIF":1.5,"publicationDate":"2020-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41941695","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: 6

Macromolecular sizes of serum albumins in its aqueous solutions 血清白蛋白水溶液中的大分子尺寸

IF 1.5

AIMS Biophysics Pub Date : 2020-06-23 DOI: 10.3934/biophy.2020017

O. Khorolskyi, N. P. Malomuzh

引用次数: 8