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Identification of gene expression signatures for psoriasis classification using machine learning techniques

Medicine in Omics 2021年 1卷

作者： Nguyen Quoc Khanh Le Duyen Thi Do Trinh-Trung-Duong Nguyen Ngan Thi Kim Nguyen Truong Nguyen Khanh Hung Nguyen Thi Thu Trang Professional Master Program in Artificial Intelligence in Medicine College of Medicine Taipei Medical University Taipei City 106 Taiwan Research Center for Artificial Intelligence in Medicine Taipei Medical University Taipei City 106 Taiwan Graduate Institute of Biomedical Informatics Taipei Medical University Taipei City 106 Taiwan Department of Computer Science and Engineering Yuan Ze University Chung-Li 32003 Taiwan School of Nutrition and Health Sciences Taipei Medical University Taipei City 110 Taiwan International Master/Ph.D. Program in Medicine College of Medicine Taipei Medical University Taipei City 110 Taiwan Orthopedic and Trauma Department Cho Ray Hospital Ho Chi Minh City Viet Nam International PhD Program for Cell Therapy and Regeneration Medicine College of Medicine Taipei Medical University Taipei City 110 Taiwan

Psoriasis classification requires the accurate identification of the lesional types for the early and effective diagnosis and it is worth interesting that the normal and psoriasis cell tissues exhibit different gene expression. Therefore, gene expression data is an effective source for psoriasis classification and there is a challenge regarding the selection of suitable gene signatures for its purpose. In this present study, the gene expression-based microarray data were used and 35 expression features linked with psoriasis were utilized to feed into our machine learning model. Overall, the performance of our model based on 35 mentioned-above features surpassed that of other state-of-the-art classifiers with an average accuracy of 98.3%, recall of 98.6%, and precision of 98% in 5-fold cross-validation tests. We also validate our model on two different sets of psoriasis and the performance results are significant. These results have suggested that our 35 expression signatures have been identified as key features for classifying samples between lesion and non-lesion. More specifically, the expression levels of few genes i.e., FABP5 , TGM1 , or BCAR3 are discovered as newly potential biomarkers for psoriasis classification and treatment with high confidence. This study, therefore, could shed light on developing the prediction models for psoriasis classification and treatment using gene expression profiles.

关键词： Psoriasis classification Random forest Gene expression Feature selection Machine learning FABP5 Dermatology

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Building 3D Profile for Lake Nubia, Using RS/GIS for Accurate Estimation of Sediment

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Procedia engineering 2017年 181卷 845-852页

作者： Mohamed Elsahabi Abdelazim Negm PhD student Civil Engineering Department Aswan University Aswan 81542 Egypt Water and Water Structures Engineering Department Faculty of Engineering Zagazig University Zagazig 44519 Egypt (Formerly at: Environmental Engineering Egypt-Japan University of Science and Technology E-JUST P.O. Box 179 New Borg El-Arab Alexandria Egypt)

Lake Nubia (LN) is the upstream part of Aswan High Dam Lake (AHDL) that lies in Sudan. This portion has been well studied; however, its bed profile had been lacking due to the lake's complex morphology. The goals of this paper are to create a 3D model robust enough to capture the lake bed heterogeneity, conduct sensitivity data processing to increase confidence in created 3D profile, and provide engineering applications of this model to aid in the management of the lake. One of these applications involved in this study is to estimate the total amount of sediments deposited in LN in order to make it possible to optimize the utilization of the sediment and accurately manage its removal in a better way. In this study, the hydrographic survey data of the lake which is conducted by using the echo-sounder via field missions and remote sensing data represented in several Landsat ETM+ images are processed and analysed by Remote Sensing and GIS software to build the 3D profiles of the lake. The method used by the Aswan High Dam Authority (AHDA) based on the complementary cross-sections is evaluated too, and its results of the accumulated sediment amount in the lake are compared with the present one that is relaying on the created 3D profiles of the lake. The results showed that the total amount of sediment in the study area till 2012 is about 5.876 billion m 3 . Also, results indicate that the present approach overestimates the sedimentation amount by about 0.22% compared to the results of the method used by AHDA. In conclusion, the created 3D model using RS/GIS captured the heterogeneity of the lake efficiently. Consequently, this model was able to analyse this morphologically complex lake.

关键词： Lake Nubia Remote Sensing GIS 3D profile Sediment amount

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Loading Dependent Electrical Properties of Hybrid Perovskite Composite Media

Loading Dependent Electrical Properties of Hybrid Perovskite...

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MRS Advances

作者： Murphy, John P. Andriolo, Jessica M. Sutton, Nathan J. Wyss, Gary Skinner, Jack L. Montana Tech Nanotechology Laboratory 1300 W. Park Street ButteMT59701 United States Materials Science PhD Program Montana State University System United States Individual Interdisiplinary PhD Program University of Montana 32 Campus Drive MissoulaMT59812 United States Mechanical Engineering Department Montana Tech 1300 W. Park Street ButteMT59701 United States Center for Advanced Mineral and Metallurgical Processing Montana Tech ButteMT59701 United States

Hybrid organic-inorganic perovskites (HOIPs) have been previously compounded with hydrophobic polymers in order to improve the resilience of HOIPs in humid environments. In this study HOIP particles were synthesized and dispersed into a polymer solution. The weight loading of the HOIP phase in the composite was increased until an abrupt change in the electrical conduction was observed indicating a percolation threshold was approached. Additionally, the CH3NH3PbI3/ polystyrene composite media was characterized to assess morphology and the effect it has on the observed electrical properties. Copyright © Materials Research Society 2017.

关键词： Perovskite

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Patterns of somatic structural variation in human cancer genomes (vol 578, pg 112, 2020)

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NATURE 2023年第7948期614卷 E38-E38页

作者： Li, Yilong Roberts, Nicola D. Wala, Jeremiah A. Shapira, Ofer Schumacher, Steven E. Kumar, Kiran Khurana, Ekta Waszak, Sebastian Korbel, Jan O. Haber, James E. Imielinski, Marcin Weischenfeldt, Joachim Beroukhim, Rameen Campbell, Peter J. Cancer Genome Project Wellcome Trust Sanger Institute Hinxton UK Totient Inc Cambridge MA USA Wellcome Sanger Institute Wellcome Genome Campus Hinxton UK Department of Haematology University of Cambridge Cambridge UK Cambridge University Hospitals NHS Foundation Trust Cambridge UK Korea Advanced Institute of Science and Technology Daejeon South Korea Department of Zoology Genetics and Physical Anthropology University of Santiago de Compostela Santiago de Compostela Spain Centre for Research in Molecular Medicine and Chronic Diseases (CIMUS) University of Santiago de Compostela Santiago de Compostela Spain The Biomedical Research Centre (CINBIO) University of Vigo Vigo Spain Centre for Research in Molecular Medicine and Chronic Diseases (CiMUS) Universidade de Santiago de Compostela Santiago de Compostela Spain Department of Zoology Genetics and Physical Anthropology (CiMUS) Universidade de Santiago de Compostela Santiago de Compostela Spain The Biomedical Research Centre (CINBIO) Universidade de Vigo Vigo Spain The Broad Institute of Harvard and MIT Cambridge MA USA Bioinformatics and Integrative Genomics Harvard University Cambridge MA USA Department of Cancer Biology Dana-Farber Cancer Institute Boston MA USA Broad Institute of MIT and Harvard Cambridge MA USA Department of Medical Oncology Dana-Farber Cancer Institute Boston MA USA Harvard Medical School Boston MA USA Massachusetts General Hospital Center for Cancer Research Charlestown MA USA Dana-Farber Cancer Institute Boston MA USA Department of Biostatistics and Computational Biology Dana-Farber Cancer Institute and Harvard Medical School Boston MA USA Weill Cornell Medical College New York NY USA Department of Physiology and Biophysics Weill Cornell Medicine New York NY USA Institute for Computational Biomedicine Weill Cornell Medicine New York NY USA Controlled Department and Institution New York NY USA Englander Institute for Precision Medicine Weill Cornell Medicine Ne

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The evolutionary history of 2,658 cancers (vol 578, pg 122, 2020)

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NATURE 2023年第7948期614卷 E42-E42页

作者： Gerstung, Moritz Jolly, Clemency Leshchiner, Ignaty Dentro, Stefan C. Gonzalez, Santiago Rosebrock, Daniel Mitchell, Thomas J. Rubanova, Yulia Anur, Pavana Yu, Kaixian Tarabichi, Maxime Deshwar, Amit Wintersinger, Jeff Kleinheinz, Kortine Vazquez-Garcia, Ignacio Haase, Kerstin Jerman, Lara Sengupta, Subhajit Macintyre, Geoff Malikic, Salem Donmez, Nilgun Livitz, Dimitri G. Cmero, Marek Demeulemeester, Jonas Schumacher, Steven Fan, Yu Yao, Xiaotong Lee, Juhee Schlesner, Matthias Boutros, Paul C. Bowtell, David D. Zhu, Hongtu Getz, Gad Imielinski, Marcin Beroukhim, Rameen Sahinalp, S. Cenk Ji, Yuan Peifer, Martin Markowetz, Florian Mustonen, Ville Yuan, Ke Wang, Wenyi Morris, Quaid D. Spellman, Paul T. Wedge, David C. Van Loo, Peter European Molecular Biology Laboratory European Bioinformatics Institute (EMBL-EBI) Cambridge UK European Molecular Biology Laboratory Genome Biology Unit Heidelberg Germany Wellcome Sanger Institute Cambridge UK Genome Biology Unit European Molecular Biology Laboratory (EMBL) Heidelberg Germany University of Ljubljana Ljubljana Slovenia The Francis Crick Institute London UK Big Data Institute University of Oxford Oxford UK Wellcome Sanger Institute Wellcome Genome Campus Hinxton UK Big Data Institute Li Ka Shing Centre University of Oxford Oxford UK University of Cambridge Cambridge UK Cambridge University Hospitals NHS Foundation Trust Cambridge UK Department of Applied Mathematics and Theoretical Physics Centre for Mathematical Sciences University of Cambridge Cambridge UK Department of Epidemiology and Biostatistics Memorial Sloan Kettering Cancer Center New York NY USA Department of Statistics Columbia University New York NY USA Department of Haematology University of Cambridge Cambridge UK University of Leuven Leuven Belgium Broad Institute of MIT and Harvard Cambridge MA USA Center for Cancer Research Massachusetts General Hospital Charlestown MA USA Department of Pathology Massachusetts General Hospital Boston MA USA Harvard Medical School Boston MA USA Center for Cancer Research Massachusetts General Hospital Boston MA USA Dana-Farber Cancer Institute Boston MA USA Department of Medical Oncology Dana-Farber Cancer Institute Boston MA USA Department of Cancer Biology Dana-Farber Cancer Institute Boston MA USA Oxford NIHR Biomedical Research Centre Oxford UK Oxford NIHR Biomedical Research Centre University of Oxford Oxford UK University of Toronto Toronto Ontario Canada Vector Institute Toronto Ontario Canada Vector Institute Toronto ON Canada Department of Computer Science University of Toronto Toronto ON Canada Ontario Institute for Cancer Research Toronto Ontario Canada University of California Los Angeles

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Sustainable and ICT-Enabled Development in Developing Areas: An E-Heritage E-Commerce Service for Handicraft Marketing

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Journal of Physics: Conference Series 2018年第1期989卷

作者： Tufail Muhammad Kwan Myung Kim PhD Candidate Graduate School of Creative Design Engineering Ulsan National 2 Institute of Science & Technology (UNIST) Ulsan South Korea Associate Professor Graduate School of Creative Design Engineering Ulsan National 2 Institute of Science & Technology (UNIST) Ulsan South Korea

Human-induced threats serve as potential hazards to cultural heritage assets, especially in developing areas where the local community, in general, is a deprived class. Sustainable tourism development is acknowledged as an economic activity to ensure careful management of assets along with local community empowerment and participation. As such, ICT-enabled development is applied in rural development projects to promote sustainable rural livelihood, but success is still limited due to a lack of community involvement and sharing in the economic gains of tourism. With this perspective in mind, the present study focuses on emerging marketing models (e-commerce) that can provide new business ventures for local communities by identifying critical online marketing elements driven by local residents.

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Author Correction: Aplp1 interacts with Lag3 to facilitate transmission of pathologic α-synuclein

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Nature communications 2024年第1期15卷 6413页

作者： Xiaobo Mao Hao Gu Donghoon Kim Yasuyoshi Kimura Ning Wang Enquan Xu Ramhari Kumbhar Xiaotian Ming Haibo Wang Chan Chen Shengnan Zhang Chunyu Jia Yuqing Liu Hetao Bian Senthilkumar S Karuppagounder Fatih Akkentli Qi Chen Longgang Jia Heehong Hwang Su Hyun Lee Xiyu Ke Michael Chang Amanda Li Jun Yang Cyrus Rastegar Manjari Sriparna Preston Ge Saurav Brahmachari Sangjune Kim Shu Zhang Yasushi Shimoda Martina Saar Haiqing Liu Sin Ho Kweon Mingyao Ying Creg J Workman Dario A A Vignali Ulrike C Muller Cong Liu Han Seok Ko Valina L Dawson Ted M Dawson Neuroregeneration and Stem Cell Programs Institute for Cell Engineering Johns Hopkins University School of Medicine Baltimore MD 21205 USA. xmao4@jhmi.edu. Department of Neurology Johns Hopkins University School of Medicine Baltimore MD 21205 USA. xmao4@jhmi.edu. Adrienne Helis Malvin Medical Research Foundation New Orleans LA 70130-2685 USA. xmao4@jhmi.edu. Neuroregeneration and Stem Cell Programs Institute for Cell Engineering Johns Hopkins University School of Medicine Baltimore MD 21205 USA. Department of Neurology Johns Hopkins University School of Medicine Baltimore MD 21205 USA. Department of Neurology Nanjing Brain Hospital Nanjing Jiangsu 210029 PR China. Medical College Yangzhou University Yangzhou Jiangsu 225001 PR China. Department of Pharmacology College of Medicine Dong-A University 32 Daesin Gongwwon-ro Seo-gu Busan 49201 Republic of Korea. Adrienne Helis Malvin Medical Research Foundation New Orleans LA 70130-2685 USA. Department of Anesthesiology West China Hospital Sichuan University. The Research Units of West China (2018RU012)-Chinese Academy of Medical Sciences West China Hospital Sichuan University Chengdu Sichuan 610041 PR China. Interdisciplinary Research Center on Biology and Chemistry Shanghai Institute of Organic Chemistry Chinese Academy of Sciences 26 Qiuyue Road Shanghai 201210 China. University of the Chinese Academy of Sciences 19 A Yuquan Road Shijingshan District Beijing 100049 China. Institute for NanoBioTechnology Johns Hopkins University Baltimore MD 21218 USA. Department of Materials Science and Engineering Whiting School of Engineering Johns Hopkins University Baltimore MD 21218 USA. Department of Brain and Cognitive Sciences Massachusetts Institute of Technology Cambridge MA 02139 USA. Picower Institute for Learning and Memory Cambridge MA 02139 USA. Harvard-MIT MD/PhD Program Harvard Medical School Boston MA 02115 USA. Department of Biological Science and Biotechnology Chungbuk Nati

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Nano oxygen particles for cell physiological condition monitoring 20

Nano oxygen particles for cell physiological condition monit...

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20th International Conference on Miniaturized Systems for Chemistry and Life sciences, MicroTAS 2016

作者： Koduri, Manohar Prasad Shao, Yu-Wei Tseng, Fan-Gang International Intercollegiate PhD Program NTHU Hsinchu Taiwan Institute of Nano Engineering and Microsystems NTHU Hsinchu Taiwan Engineering and System Science NTHU Hsinchu Taiwan

ISBN: (纸本)9780979806490

In this study we demonstrate a novel Nano-particle (NP) oxygen sensors for monitoring in vitro oxygen concentration/distribution by measuring the fluorescence intensity in HeLa cells filled alginate hydrogel sphere. The Nano Oxygen Particles (NOP) are made by conjugating oxygen sensitive fluorescence dye through the mediation of amphiphilic linkers on Polystyrene bead (PSB, 510nm in diameter) surface, as shown in figure 1.

关键词： Fluorescence

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Application of space syntax method to measure spatial connectivity in campus of Institut Teknologi Sepuluh Nopember (ITS)

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IOP Conference Series: Earth and Environmental science 2018年第1期202卷

作者： A M Navastara M Yusuf P Navitas Department of Regional and Urban Planning Faculty of Architecture Design and Planning Institut Teknologi Sepuluh Nopember Kampus ITS Sukolilo-Surabaya 60111 Indonesia PhD Candidate School of Civil Engineering and Built Environment Science and Engineering Faculty Queensland University of Technology Australia

In line with ITS's vision to create an eco-friendly campus, there is an effort to decrease the use of private vehicles in ITS campus. The role of pedestrian lanes is very important to encourage and support eco-friendly transportation in campus area. Transportation system should be supported by mode of transport with equal, feasible, and humane pedestrian lane. ITS has already begun to develop pedestrian lanes in parts of their campus. Ideally, the development of pedestrian lanes should be linked to form a network, connecting centres of activities. Therefore, the aim of this research is to determine the level of connectivity of pedestrian ways in ITS's Sukolilo campus area as an input for future development of pedestrian lanes. This study employed on-site observations and connectivity calculations by way of Space Syntax. Analysis shows that 70% of pedestrian ways in the Sukolilo campus are of very low connectivity. This is due to unintegrated pedestrian lanes and poorly coordinated campus development.

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Current findings on terrestrial plants – Engineered nanomaterial interactions: Are plants capable of phytoremediating nanomaterials from soil?

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Current Opinion in Environmental science and Health 2018年 6卷 9-15页

作者： Cota-Ruiz, Keni Delgado-Rios, Marcos Martínez-Martínez, Alejandro Núñez-Gastelum, José Alberto Peralta-Videa, Jose Ramon Gardea-Torresdey, Jorge Luis Department of Chemistry The University of Texas at El Paso 500 West University Avenue El Paso 79968 TX United States Departamento de Ciencias Químico Biológicas Instituto de Ciencias Químico Biológicas Universidad Autónoma de Ciudad Juárez Anillo Envolvente del PRONAF y Estocolmo S/n Ciudad Juárez Chihuahua 32310 Mexico El Colegio de Chihuahua Calle Partido Díaz 4723 Esquina con Anillo Envolvente del PRONAF Ciudad Juárez Chihuahua 32310 Mexico Environmental Science and Engineering PhD Program Department of Chemistry The University of Texas at El Paso 500 West University Avenue El Paso 79968 TX United States UC Center for Environmental Implications of Nanotechnology (UC CEIN) The University of Texas at El Paso 500 West University Avenue El Paso 79968 TX United States

Engineered Nanomaterials (ENMs) are revolutionizing our daily lives, industry, and agriculture. Along with their novel applications, major concerns have emerged due to the potential toxicity to biological systems. Since soils are considered the main destination for ENMs, research focused on their interaction with plants is gaining more attention, especially at the physiological and biochemical levels. This review addresses the capacity of some plants to accumulate ENMs or released ions, highlighting the beneficial and detrimental effects and the potential use of some plants to remediate ENM-contaminated environments. Although the uptake process depends on multiple factors, the literature suggests that concentrations <50 mg/kg are beneficial, while higher doses negatively impact physiological and biochemical parameters. However, the current data does not allow the formulation of mechanistic model effects. Finally, this review remarks on the pivotal role played by plants as a sustainable alternative to face the environmental buildup of ENMs and to guarantee food security. © 2018 Elsevier B.V.

关键词： Biotransformation ENM-plant interactions Food security Phytoremediation Risk assessment

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