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K-Means Clustering Model to Discriminate Copper-Resistant Bacteria as Bioremediation Agents

Procedia computer science 2021年 179卷 804-812页

作者： Ika Nurlaila Wahyu Irawati Kartika Purwandari Bens Pardamean Information Systems Department BINUS Online Learning Bina Nusantara University Jakarta Indonesia 11480 Department of Biology Education Faculty of Education Pelita Harapan University Tangerang Indonesia 15811 Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia 11480 Computer Science Department BINUS Graduate Program - Master of Computer Science Bina Nusantara University Jakarta Indonesia 11480

Copper (Cu) has been excessively used for some valuable commodities and this creates environmental problems. The inorganic element becomes toxic when presents beyond the recommended tolerated concentration. Bacterial-based remediation is seen to be an excellent tool to overcome it as it reduces the copper contamination without yielding any other forms of contamination. There are some pivotal properties in the bacteria render them being considered as bioremediation agents against coppers contamination, namely bioaccumulation and biosorption. In the present study, we question if these bacteria could be clustered into a strong and representative proximity according to their functional properties. Mostly, bacteria are grouped based on their genetic profiles derived from the 16S rRNA sequencing. We propose that our K-Means clustering model can be employed to identify genetically-unlabelled bacteria. But first, a prominent reference should be developed and we are in this phase. We figured out the K-Means clustering model do not pull the same-genus bacteria into the same cluster. Instead, the model gathers into a proximity those isolates with similarity on a functional characteristic termed minimum inhibitory concentration (MIC), regardless their origins and their hierarchy in taxonomy.

关键词： Copper-Resistant Bacteria K-Means Minimum Inhibitory Concentration

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Statistical Power Analysis for Designing Bulk, Single-Cell, and Spatial Transcriptomics Experiments: Review, Tutorial, and Perspectives

arXiv

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arXiv 2023年

作者： Jeon, Hyeongseon Xie, Juan Jeon, Yeseul Jung, Kyeong Joo Gupta, Arkobrato Chang, Won Chung, Dongjun Department of Biomedical Informatics The Ohio State University ColumbusOH United States Pelotonia Institute for Immuno-Oncology The James Comprehensive Cancer Center The Ohio State University ColumbusOH43210 United States The Interdisciplinary PhD program in Biostatistics The Ohio State University ColumbusOH United States Department of Statistics and Data Science Yonsei University Seoul Korea Republic of Department of Applied Statistics Yonsei University Seoul Korea Republic of Department of Computer Science and Engineering The Ohio State University ColumbusOH United States Division of Statistics and Data Science University of Cincinnati CincinnatiOH United States

Gene expression profiling technologies have been used in various applications such as cancer biology. The development of gene expression profiling has expanded the scope of target discovery in transcriptomic studies, and each technology produces data with distinct characteristics. In order to guarantee biologically meaningful findings using transcriptomic experiments, it is important to consider various experimental factors in a systematic way through statistical power analysis. In this paper, we review and discuss the power analysis for three types of gene expression profiling technologies from a practical standpoint, including bulk RNA-seq, single-cell RNA-seq, and high-throughput spatial transcriptomics. Specifically, we describe the existing power analysis tools for each research objective for each of the bulk RNA-seq and scRNA-seq experiments, along with recommendations. On the other hand, since there are no power analysis tools for high-throughput spatial transcriptomics at this point, we instead investigate the factors that can influence power analysis. © 2023, CC BY-NC-ND.

关键词： RNA

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Ultrastrong Spin-Photon Coupling in Gadolinium Gallium Garnet

Ultrastrong Spin-Photon Coupling in Gadolinium Gallium Garne...

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2023 Conference on Lasers and Electro-Optics, CLEO 2023

作者： Kritzell, T. Elijah Bao, Junzhe Doumani, Jacques Lee, Jae Joon Xu, Hongjing Tay, Fuyang Nojiri, Hiroyuki Bamba, Motoaki Baydin, Andrey Kono, Junichiro Department of Electrical and Computer Engineering Rice University HoustonTX77005 United States Applied Physics Graduate Program Smalley-Curl Institute Rice University HoustonTX77005 United States Department of Physics and Astronomy Rice University HoustonTX77005 United States Institute for Materials Research Tohoku University Sendai980-8577 Japan The Hakubi Center for Advanced Research Kyoto University Kyoto606-8502 Japan Department of Physics I Kyoto University Kyoto606-8502 Japan Smalley-Curl Institute Rice University HoustonTX77005 United States Department of Material Science and NanoEngineering Rice University HoustonTX77005 United States

We examine ultrastrong coupling of an ensemble of paramagnetic spins in Gd3Ga5O12 with terahertz photons in the presence of a high external magnetic field both in the bulk and thin-film limits. © 2023 The Author(s)

ISBN: (纸本)9781957171258

关键词： Photons

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The by-product of oil palm dosage application on Turnera subulata growth supports water supply

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AIP Conference Proceedings 2024年第1期3026卷

作者： Pauliz Budi Hastuti Gilang Tri Anggara Wiwin Dyah Ully Parwati Teddy Suparyanto Digdo Sudigyo Bens Pardamean Faculty of Agriculture STIPER Institute of Agriculture Yogyakarta Indonesia 55281 Faculty of Agricultural Technology STIPER Institute of Agriculture Yogyakarta Indonesia 55281 Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia 11480 Computer Science Department BINUS Graduate Program - Master of Computer Science Program Bina Nusantara University Jakarta Indonesia 11480

Plant growth with complex organic matter content can be enhanced by using oil palm by-products. These organic materials can maintain the water supply in the plant body. Therefore, in oil palm plantations with significant groundwater consumption, organic matter’s the ability to sustain water availability. Caterpillars that devour palm leaves are among the numerous pests that threaten oil palm plantations. Predators of leaf-eating caterpillars use the holly rose flower (Turnera subulata) in oil palm farms as a habitat. Therefore, the effect of the type and dose treatment of oil palm by-products on the growth of Turnera subulata was observed to support sustainable water management in oil palm plantations. The research was carried out using a factorial design arranged in a Completely Randomized Design (CRD) consisting of two components: the type of palm oil mill by-product (boiler ash, empty bunches, and solid) and the dose of a by-product (% volume) consisting of four dosages (0, 25, 33, and 50% volume). The research data were analyzed using variance at the 5% test level. A DMRT test at the 5% test level was conducted on the treatment that had a significant effect. The growth of Turnera subulata was most positively impacted by a solid application dose of 50% volume. Turnera subulata plants responded the least favorably to the application of empty bunches in any dose treatment.

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Improving quantitation accuracy in isobaric-labeling mass spectrometry experiments with spectral library searching and feature-based peptide-spectrum match filter

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Scientific Reports 2023年第1期13卷 1-10页

作者： Kuo, Tzu-Yun Wang, Jen-Hung Huang, Yung-Wen Sung, Ting-Yi Chen, Ching-Tai Department of Biochemical Science and Technology National Taiwan University Taipei 10617 Taiwan Bioinformatics Program Taiwan International Graduate Program Institute of Statistical Science Academia Sinica Taipei 11529 Taiwan Institute of Information Science Academia Sinica Taipei 11529 Taiwan Institute of Biomedical Informatics National Yang Ming Chiao Tung University Taipei 11221 Taiwan Department of Computer Science and Information Engineering National Taiwan University Taipei 10617 Taiwan Department of Bioinformatics and Biomedical Engineering Asia University Taichung 41354 Taiwan Center for Precision Health Research Asia University Taichung 41354 Taiwan

Isobaric labeling relative quantitation is one of the dominating proteomic quantitation technologies. Traditional quantitation pipelines for isobaric-labeled mass spectrometry data are based on sequence database searching. In this study, we present a novel quantitation pipeline that integrates sequence database searching, spectral library searching, and a feature-based peptide-spectrum-match (PSM) filter using various spectral features for filtering. The combined database and spectral library searching results in larger quantitation coverage, and the filter removes PSMs with larger quantitation errors, retaining those with higher quantitation accuracy. Quantitation results show that the proposed pipeline can improve the overall quantitation accuracy at the PSM and protein levels. To our knowledge, this is the first study that utilizes spectral library searching to improve isobaric labeling-based quantitation. For users to conveniently perform the proposed pipeline, we have implemented the feature-based filter being executable on both Windows and Linux platforms;its executable files, user manual, and sample data sets are freely available at https://***/comics/Software_*** . Furthermore, with the developed filter, the proposed pipeline is fully compatible with the Trans-Proteomic Pipeline. © 2023, Springer Nature Limited.

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Maximum A-Posteriori Probability (MAP) Terahertz Parameter Extraction for Pancreatic Ductal Adenocarcinoma

Maximum A-Posteriori Probability (MAP) Terahertz Parameter E...

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International Conference on Infrared and Millimeter Waves

作者： Debamitra Chakraborty Bradley N. Mills Jing Cheng Scott A. Gerber Roman Sobolewski Materials Science Graduate Program University of Rochester Rochester New York USA Laboratory for Laser Energetics University of Rochester Rochester New York USA Department of Surgery University of Rochester Medical Center Rochester New York USA Department of Electrical and Computer Engineering University of Rochester Rochester New York USA

ISBN: (数字)9781728194271

ISBN: (纸本)9781728194288

We developed a maximum a-posteriori probability-based terahertz parameter extraction method to obtain tissue characteristics of paraffin-embedded murine pancreatic ductal adenocarcinoma samples. This estimation algorithm can produce conservative estimates of tissue parameters without resorting to frequency-domain analysis. We report well-resolved and statistically significant differences in tumor tissue regions as compared to their healthy counterparts using our parameters extraction algorithm. We propose to use the index of refraction and the absorption as imaging biomarker parameters for biological tissue characterization.

关键词： Maximum a posteriori estimation Absorption Frequency-domain analysis Biological tissues Refractive index Estimation Probability

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Broadband Coherent Wave Control Through Photonic Collisions at Time Interfaces

arXiv

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arXiv 2022年

作者： Galiffi, Emanuele Xu, Gengyu Yin, Shixiong Moussa, Hady Ra'di, Younes Alù, Andrea Photonics Initiative Advanced Science Research Center City University of New York 85 St. Nicholas Terrace New York10031 United States Department of Electrical Engineering City College City University of New York United States Physics Program Graduate Center City University of New York United States Department of Electrical Engineering and Computer Science Syracuse University SyracuseNY13244 United States

Coherent wave control exploits the interference among multiple waves impinging on a system to suppress or enhance outgoing signals based on their relative phase and amplitude. This process inherently requires the combination of non-Hermiticity, in order to enable energy exchanges among the waves, and spatial interfaces in order to tailor their scattering. Here we explore the temporal analogue of this phenomenon, based on time-interfaces that support instantaneous non-Hermitian scattering events for photons. Based on this mechanism, we demonstrate ultra-broadband temporal coherent wave control and the photonic analogue of mechanical collisions with phase-tunable elastic features. We apply them to erase, enhance and reshape arbitrary pulses by suitably tailoring the amplitude and phase of counterpropagating signals. Our findings provide a pathway to effectively sculpt broadband light with light without requiring spatial boundaries, within an ultrafast and low-energy platform. © 2022, CC BY.

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LOCI: A Mobile QA System with Multimodal Motivation Scheme for Local Intent Questions in Dynamic Social Networks 91

LOCI: A Mobile QA System with Multimodal Motivation Scheme f...

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91st IEEE Vehicular Technology Conference, VTC Spring 2020

作者： Ali, Imad Chang, Ronald Y. Hsu, Cheng-Hsin Lee, Chi-Han Institute of Information Science Academia Sinica Taiwan International Graduate Program Social Networks and Human-Centered Computing Taipei Taiwan Research Center for Information Technology Innovation Academia Sinica Taipei Taiwan National Tsing Hua University Department of Computer Science Hsinchu Taiwan

ISBN: (纸本)9781728152073

Recent research has shown that people are frequently searching for information with local intent. The existing systems fail to answer this class of questions as they are not mainly designed to handle it. In this paper, we propose LOCI, a mobile question answer system with a multimodal motivation scheme for local intent questions where users provide timely and accurate answers in a dynamic social network. LOCI mines users' shared and contextual information to identify the most relevant users for each question. The proposed multimodal motivation scheme exploits users' social ties and monetary rewards to raise their basic motivation levels. LOCI assigns questions to the best answerers via our three proposed algorithms: (i) LOCI-RT, which immediately assigns newly arrived questions/users to available users/questions, (ii) LOCI-LO, which uses short-time batches for locally optimal questions-users assignment, and (iii) LOCI-AD, which assigns short- and long-deadline questions immediately and via batching, respectively. We conduct: (i) a survey to support our assumptions regarding the proposed multimodal motivation scheme, and (ii) trace-driven experiments to evaluate the performance of the three proposed LOCI's algorithms. © 2020 IEEE.

关键词： Motivation

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NTRK3 exhibits a pro-oncogenic function in upper tract urothelial carcinomas

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Kaohsiung Journal of Medical sciences 2024年第5期40卷 445-455页

作者： Lim, Lee-Moay Lee, Yi-Chen Lin, Ting-Wei Hong, Zi-Xuan Hsu, Wei-Chi Ke, Hung-Lung Hwang, Daw-Yang Chung, Wen-Yu Li, Wei-Ming Lin, Hui-Hui Kuo, Hung-Tien Huang, A-Mei Graduate Institute of Clinical Medicine College of Medicine Kaohsiung Medical University Kaohsiung Taiwan Division of Nephrology Department of Internal Medicine Kaohsiung Medical University Hospital Kaohsiung Medical University Kaohsiung Taiwan School of Medicine College of Medicine Kaohsiung Medical University Kaohsiung Taiwan Graduate Institute of Medicine College of Medicine Kaohsiung Medical University Kaohsiung Taiwan Department of Anatomy School of Medicine College of Medicine Kaohsiung Medical University Kaohsiung Taiwan Department of Urology School of Medicine College of Medicine Kaohsiung Medical University Kaohsiung Taiwan Department of Urology Kaohsiung Medical University Hospital Kaohsiung Medical University Kaohsiung Taiwan Department of Urology Kaohsiung Municipal Ta-Tung Hospital Kaohsiung Medical University Kaohsiung Taiwan National Institute of Cancer Research National Health Research Institute Tainan Taiwan Department of Computer Science and Information Engineering National Kaohsiung University of Science and Technology Kaohsiung Taiwan Department of Urology Ministry of Health and Welfare Pingtung Hospital Pingtung Taiwan Department of Medical Research Kaohsiung Medical University Hospital Kaohsiung Medical University Kaohsiung Taiwan Doctoral Degree Program in Toxicology College of Pharmacy Kaohsiung Medical University Kaohsiung Taiwan Department of Biochemistry School of Medicine College of Medicine Kaohsiung Medical University Kaohsiung Taiwan Research Center for Environmental Medicine Kaohsiung Medical University Kaohsiung Taiwan

Neurotrophic receptor tyrosine kinase 3 (NTRK3) has pleiotropic functions: it acts not only as an oncogene in breast and gastric cancers but also as a dependence receptor in tumor suppressor genes in colon cancer and neuroblastomas. However, the role of NTRK3 in upper tract urothelial carcinoma (UTUC) is not well documented. This study investigated the association between NTRK3 expression and outcomes in UTUC patients and validated the results in tests on UTUC cell lines. A total of 118 UTUC cancer tissue samples were examined to evaluate the expression of NTRK3. Survival curves were generated using Kaplan–Meier estimates, and Cox regression models were used for investigating survival outcomes. Higher NTRK3 expression was correlated with worse progression-free survival, cancer-specific survival, and overall survival. Moreover, the results of an Ingenuity Pathway Analysis suggested that NTRK3 may interact with the PI3K-AKT-mTOR signaling pathway to promote cancer. NTRK3 downregulation in BFTC909 cells through shRNA reduced cellular migration, invasion, and activity in the AKT-mTOR pathway. Furthermore, the overexpression of NTRK3 in UM-UC-14 cells promoted AKT-mTOR pathway activity, cellular migration, and cell invasion. From these observations, we concluded that NTRK3 may contribute to aggressive behaviors in UTUC by facilitating cell migration and invasion through its interaction with the AKT-mTOR pathway and the expression of NTRK3 is a potential predictor of clinical outcomes in cases of UTUC. © 2024 The Authors. The Kaohsiung Journal of Medical sciences published by John Wiley & Sons Australia, Ltd on behalf of Kaohsiung Medical University.

关键词： AKT-mTOR pathway neurotrophic receptor tyrosine kinase 3 (NTRK3) prognosis tropomyosin-related kinase (TrK) upper tract urothelial carcinoma (UTUC)

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Technology Roadmap for Flexible Sensors

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ACS NANO 2023年第6期17卷 5211-5295页

作者： Luo, Yifei Abidian, Mohammad Reza Ahn, Jong-Hyun Akinwande, Deji Andrews, Anne M. Antonietti, Markus Bao, Zhenan Berggren, Magnus Berkey, Christopher A. Bettinger, Christopher John Chen, Jun Chen, Peng Cheng, Wenlong Cheng, Xu Choi, Seon-Jin Chortos, Alex Dagdeviren, Canan Dauskardt, Reinhold H. Di, Chong-an Dickey, Michael D. Duan, Xiangfeng Facchetti, Antonio Fan, Zhiyong Fang, Yin Feng, Jianyou Feng, Xue Gao, Huajian Gao, Wei Gong, Xiwen Guo, Chuan Fei Guo, Xiaojun Hartel, Martin C. He, Zihan Ho, John S. Hu, Youfan Huang, Qiyao Huang, Yu Huo, Fengwei Hussain, Muhammad M. Javey, Ali Jeong, Unyong Jiang, Chen Jiang, Xingyu Kang, Jiheong Karnaushenko, Daniil Khademhosseini, Ali Kim, Dae-Hyeong Kim, Il-Doo Kireev, Dmitry Kong, Lingxuan Lee, Chengkuo Lee, Nae-Eung Lee, Pooi See Lee, Tae-Woo Li, Fengyu Li, Jinxing Liang, Cuiyuan Lim, Chwee Teck Lin, Yuanjing Lipomi, Darren J. Liu, Jia Liu, Kai Liu, Nan Liu, Ren Liu, Yuxin Liu, Yuxuan Liu, Zhiyuan Liu, Zhuangjian Loh, Xian Jun Lu, Nanshu Lv, Zhisheng Magdassi, Shlomo Malliaras, George G. Matsuhisa, Naoji Nathan, Arokia Niu, Simiao Pan, Jieming Pang, Changhyun Pei, Qibing Peng, Huisheng Qi, Dianpeng Ren, Huaying Rogers, John A. Rowe, Aaron Schmidt, Oliver G. Sekitani, Tsuyoshi Seo, Dae-Gyo Shen, Guozhen Sheng, Xing Shi, Qiongfeng Someya, Takao Song, Yanlin Stavrinidou, Eleni Su, Meng Sun, Xuemei Takei, Kuniharu Tao, Xiao-Ming Tee, Benjamin C. K. Thean, Aaron Voon-Yew Trung, Tran Quang Wan, Changjin Wang, Huiliang Wang, Joseph Wang, Ming Wang, Sihong Wang, Ting Wang, Zhong Lin Weiss, Paul S. Wen, Hanqi Xu, Sheng Xu, Tailin Yan, Hongping Yan, Xuzhou Yang, Hui Yang, Le Yang, Shuaijian Yin, Lan Yu, Cunjiang Yu, Guihua Yu, Jing Yu, Shu-Hong Yu, Xinge Zamburg, Evgeny Zhang, Haixia Zhang, Xiangyu Zhang, Xiaosheng Zhang, Xueji Zhang, Yihui Zhang, Yu Zhao, Siyuan Zhao, Xuanhe Zheng, Yuanjin Zheng, Yu-Qing Zheng, Zijian Zhou, Tao Zhu, Bowen Zhu, Ming Zhu, Rong Zhu, Yangzhi Zhu, Yong Zou, Guijin Chen, Xiaodong 08-03 Innovis Singapore 138634 Republic of Singapore Innovative Centre for Flexible Devices (iFLEX) School of Materials Science and Engineering Nanyang Technological University Singapore 639798 Singapore Department of Biomedical Engineering University of Houston Houston Texas 77024 United States School of Electrical and Electronic Engineering Yonsei University Seoul 03722 Republic of Korea Department of Electrical and Computer Engineering The University of Texas at Austin Austin Texas 78712 United States Microelectronics Research Center The University of Texas at Austin Austin Texas 78758 United States Department of Chemistry and Biochemistry California NanoSystems Institute and Department of Psychiatry and Biobehavioral Sciences Semel Institute for Neuroscience and Human Behavior and Hatos Center for Neuropharmacology University of California Los Angeles Los Angeles California 90095 United States Colloid Chemistry Department Max Planck Institute of Colloids and Interfaces 14476 Potsdam Germany Department of Chemical Engineering Stanford University Stanford California 94305 United States Laboratory of Organic Electronics Department of Science and Technology Campus Norrköping Linköping University 83 Linköping Sweden Wallenberg Initiative Materials Science for Sustainability (WISE) and Wallenberg Wood Science Center (WWSC) SE-100 44 Stockholm Sweden Department of Materials Science and Engineering Stanford University Stanford California 94301 United States Department of Biomedical Engineering and Department of Materials Science and Engineering Carnegie Mellon University Pittsburgh Pennsylvania 15213 United States Department of Bioengineering University of California Los Angeles Los Angeles California 90095 United States School of Chemistry Chemical Engineering and Biotechnology Nanyang Technological University Singapore 637457 Singapore Nanobionics Group Department of Chemical and Biological Engineering Monash University Clayton Australia 3800 Monash

Humans rely increasingly on sensors to address grand challenges and to improve quality of life in the era of digitalization and big data. For ubiquitous sensing, flexible sensors are developed to overcome the limitations of conventional rigid counterparts. Despite rapid advancement in bench-side research over the last decade, the market adoption of flexible sensors remains limited. To ease and to expedite their deployment, here, we identify bottlenecks hindering the maturation of flexible sensors and propose promising solutions. We first analyze continued...challenges in achieving satisfactory sensing performance for real-world applications and then summarize issues in compatible sensor-biology interfaces, followed by brief discussions on powering and connecting sensor networks. Issues en route to commercialization and for sustainable growth of the sector are also analyzed, highlighting environmental concerns and emphasizing nontechnical issues such as business, regulatory, and ethical considerations. Additionally, we look at future intelligent flexible sensors. In proposing a comprehensive roadmap, we hope to steer research efforts towards common goals and to guide coordinated development strategies from disparate communities. Through such collaborative

关键词： soft materials mechanics engineering flexible electronics conformable sensors bioelectronics human-machine interfaces body area sensor networks technology translation sustainable electronics

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