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3rd International Conference on Eco Engineering Development, ICEED 2019

作者： Pardamean, Bens Cenggoro, Tjeng Wawan Chandra, Bloomest Jansen Rahutomo, Reza Computer Science Department BINUS Graduate Program Master of Computer Science Program Bina Nusantara University Jakarta11480 Indonesia Computer Science Department School of Computer Science Bina Nusantara University Jakarta11480 Indonesia Computer Science Department College of Letters and Science University of Wisconsin MadisonWI53706 United States Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta11480 Indonesia

The concept of smart building includes the optimization of energy usage in a building. One of the possible solutions for this is to adaptively adjust appliances utilization according to activity level in the building. Thus, an intelligent activity estimation system needs to be developed. However, massive annotated dataset is necessary to train the system. Therefore, we propose a system that enables rapid data annotation to collect the massive dataset. With the proposed system, an image can be annotated within 4.8 seconds in average. © 2020 Published under licence by IOP Publishing Ltd.

关键词： Historic preservation

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Differentiation and Integration of Machine Learning Feature Vectors

Differentiation and Integration of Machine Learning Feature ...

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International Conference on Machine Learning and Applications (ICMLA)

作者： Xinying Mu Ana B. Pavel Mark Kon Department of Mathematics and Statistics Boston University Boston MA Graduate Program in Bioinformatics Boston University Boston MA Section of Computational Biomedicine School of Medicine Boston MA

ISBN: (纸本)9781509061686

This paper presents a new approach to the production of feature maps for the improvement of classification in machine learning. The idea is based on a calculus of differentiation and integration of feature vectors, which can be viewed as functions on a metric space or network. Based on this we propose a novel network-based binary machine learning classifier. We illustrate our method using molecular networks alone to distinguish phenotypes, including cancer types and subtypes. We include feature sets derived from disease-specific gene co-expression networks in different cancer data sets using The Cancer Genome Atlas (TCGA) along with other previously published studies. We also illustrate our network-based predictor on another data type, based on infrared spectroscopy of lung cancer tissue.

关键词： Cancer Gene expression Correlation Lungs Kernel Laplace equations Proteins

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Lateral transfer of mRNA and protein by migrasomes modifies the recipient cells

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细胞研究（英文版） 2021年第2期31卷 237-240页

作者： Mingli Zhu Qin Zou Rongyao Huang Ying Li Xudong Xing Jianhuo Fang Liang Ma Lifei Li Xuerui Yang Li Yu State Key Laboratory of Membrane Biology Tsinghua University-Peking University Joint Center for Life Sciences Beijing Frontier Research Center for Biological Structure School of Life ScienceTsinghua University Beijing 100084 China Joint Graduate Program of Peking-Tsinghua-National Institute of Biological Science Tsinghua University Beijing 100084 China Joint Graduate Program of Peking-Tsinghua-National Institute of Biological Science Tsinghua University Beijing 100084 China MOE Key Laboratory of Bioinformatics Tsinghua University Center for Synthetic & Systems Biology Tsinghua University School of Life Science Beijing 100084China State Key Laboratory of Membrane Biology Tsinghua University-Peking University Joint Center for Life Sciences Beijing Frontier Research Center for Biological Structure School of Life ScienceTsinghua University Beijing 100084 China MOE Key Laboratory of Bioinformatics Tsinghua University Center for Synthetic & Systems Biology Tsinghua University School of Life Science Beijing 100084China

Dear Editor,Migrasomes are recently discovered vesicular organelles which form on the retraction fibers(RFs)of migrating cells.1 Once detached from cells,migrasomes can rupture and release their luminal contents1 in a process named ***,migrasomes have been shown to play an important role in zebrafish organ morphogenesis by releasing chemokine signals to defined regions of the embryo.2 Thus,migracytosis is considered as a major mechanism for migrasomes to carry out their *** has been frequently observed that intact migrasomes can be engulfed by surrounding cells,1 and this has been proposed as a potential mechanism for lateral transfer of cellular contents between ***,it is not clear whether the lateral transfer of cellular contents by migrasomes has functional consequences for the recipient cells.

关键词： Extracellular signalling molecules Organelles

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Chirality provides a direct fitness advantage and facilitates intermixing in cellular aggregates

arXiv

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arXiv 2017年

作者： George, Ashish B. Korolev, Kirill S. Department of Physics Boston University BostonMA02215 United States Department of Physics Graduate Program in Bioinformatics Boston University BostonMA02215 United States

Short Abstract: Is it better to be left- or right-handed? The answer depends on whether the goal is making a handshake or winning a boxing match. The need for coordination favors the handedness of the majority, but being different could also provide an advantage. The same rules could apply to microbial colonies and cancer tumors. Like humans, cells often have handedness (chirality) that reflects the lack of mirror symmetry in their shapes or movement patterns. We find that cells gain a substantial fitness advantage by either increasing the magnitude of their chirality or switching to the opposite handedness. Selection for specific chirality is mediated by the formation of bulges along the colony edge in regions where cells with different chiralities meet. Long Abstract: Chirality in shape and motility can evolve rapidly in microbes and cancer cells. To determine how chirality affects cell fitness, we developed a model of chiral growth in compact aggregates such as microbial colonies and solid tumors. Our model recapitulates previous experimental findings and shows that mutant cells can invade by increasing their chirality or switching their handedness. The invasion results either in a takeover or stable coexistence between the mutant and the ancestor depending on their relative chirality. For large chiralities, the coexistence is accompanied by strong intermixing between the cells, while spatial segregation occurs otherwise. We show that the competition within the aggregate is mediated by bulges in regions where the cells with different chiralities meet. The two-way coupling between aggregate shape and natural selection is described by the chiral Kardar-Parisi-Zhang equation coupled to the Burgers' equation with multiplicative noise. We solve for the key features of this theory to explain the origin of selection on chirality. Overall, our work suggests that chirality could be an important ecological trait that mediates competition, invasion, and spatial structure in

关键词： Chirality

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Maintaining the Quality and Aroma of Coffee with Fuzzy Logic Coffee Roasting Machine 3

Maintaining the Quality and Aroma of Coffee with Fuzzy Logic...

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3rd International Conference on Eco Engineering Development, ICEED 2019

作者： Harsawardana Samodro, Bayu Mahesworo, Bharuno Suparyanto, Teddy Surya Atmaja, Don Bosco Pardamean, Bens Institut Pertanian STIPER Yogyakarta55281 Indonesia Mechatronics and AI Research and Development Center Biotechnic Innovation Yogyakarta55281 Indonesia Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta11480 Indonesia Computer Science Department BINUS Graduate Program - Master of Computer Science Bina Nusantara University Jakarta11480 Indonesia

With the increasing global demands of coffee, Indonesia need to increase their coffee beans supply and improve the quality to maintain its position in the international coffee industry. One of the most important coffeepre-processing, coffee bean roasting, is under developed in Indonesia. Indonesia coffee farmers prefer to use the traditional cauldron to roast their coffee beans. Roasting coffee beans using traditional cauldron is inefficient and resulting unequal roasted level for the coffee beans. In this study, we proposed atemperature control system based on fuzzy logic for coffee roaster machine. The system controls the temperature in accordance with the demanded roasting level. A thermal camera is attached inside the roasting chamber to monitor the heaton the roasted coffee beans. The thermal camera is integrated with a stirring mechanism to equalise the heat among the beans. © 2020 Published under licence by IOP Publishing Ltd.

关键词： Fuzzy logic

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A zinc finger-dependent, PRDM13-driven mechanism regulates retinal progenitor cell fate from mouse embryonic stem cells via WNT signaling

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Stem Cell Reports 2025年 102508页

作者： Brian W. Basinski Yuanhao Huang Qiang Li Charukesi D. Sivakumar Tyler J. Carman Hana M. Pan Jing Xu D. Ford Hannum Jie Liu Rajesh C. Rao Department of Ophthalmology and Visual Science W.K. Kellogg Eye Center University of Michigan Ann Arbor MI 48105 USA Molecular and Cellular Pathology Graduate Program Department of Pathology University of Michigan Ann Arbor MI 48105 USA Department of Computational Medicine and Bioinformatics Ann Arbor MI 48105 USA Department of Human Genetics University of Michigan Ann Arbor MI 48105 USA Rogel Cancer Center University of Michigan Ann Arbor MI 48105 USA Center of Computational Medicine and Bioinformatics University of Michigan Ann Arbor MI 48105 USA Center for RNA Biomedicine University of Michigan Ann Arbor MI 48105 USA A. Alfred Taubman Medical Research Institute University of Michigan Ann Arbor MI 48105 USA Section of Ophthalmology Surgical Service Veterans Administration Ann Arbor Healthcare System Ann Arbor MI 48105 USA

The transcriptional regulation underlying eye field (retinal primordium) development requires precise control, yet the mechanisms guiding lineage-specific differentiation within the central nervous system (CNS) remain incompletely understood. Using neuroectoderm (NE) organoids derived from mouse embryonic stem cells, we investigate the role of PRDM13 in eye field specification. We demonstrate that Prdm13 expression inhibits RX + eye field fate but permits non-eye field NE differentiation, an effect that depends on its first and second zinc-finger domains. Prdm13 activates the WNT/β-catenin signaling pathway during differentiation, leading to downregulation of key transcription factors crucial for establishing the eye field. Pharmacological inhibition of WNT signaling abolishes PRDM13-mediated suppression, restoring RX + eye field differentiation. Our work reveals a previously undescribed PRDM13-WNT signaling axis that regulates lineage-specific neural differentiation of embryonic stem cells.

关键词： stem cells organoids retinal development WNT PRDM13

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LLM2Vec Sentence Embeddings Analysis in Sentiment Classification

LLM2Vec Sentence Embeddings Analysis in Sentiment Classifica...

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2024 IEEE International Conference on Data and Software Engineering, ICoDSE 2024

作者： Henry, Matthew Martianus Heryanto, Nur Adhianti Isnan, Mahmud Kurnianingrum, Dian Ratnapuri, Chyntia Ika Pardamean, Bens Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta11480 Indonesia Computer Science Department School of Computer Science Bina Nusantara University Jakarta11480 Indonesia Entrepreneurship Department Bina Nusantara University Jakarta11480 Indonesia Computer Science Department BINUS Graduate Program Bina Nusantara University Jakarta11480 Indonesia

ISBN: (纸本)9798331506407

Sentiment analysis is crucial method in business intelligence to extract insights, which typically begin with sentiment classification. One of the latest frameworks for generating sentence embeddings for sentiment classification is LLM2Vec, which allows Transformer decoder-based models to generate sentence embeddings for text representation. Its capability is deemed language-agnostic, which, in this study, the framework is leveraged for Tokopedia tweet sentiment analysis to prove the claim. The base decoder models used in the LLM2Vec framework were Llama 3 8B, Llama 2 7B, Sheared Llama 1.3B, and Mistral 7B. Two BERT-based models, which are the Indonesian SBERT model and IndoBERT trained with the SimCSE approach, were employed as a comparison. The generated embeddings were classified using logistic regression, SVM, and MLP Classifier. Classifiers using embedding generated by LLM2Vec with Llama 3 8B and Mistral 7B achieves on-par performance with classifiers that utilize IndoBERT SimCSE embeddings, while classifiers using embeddings generated by LLM2Vec with Llama 2 7B and Sheared Llama 1.3B achieves much lower performance. Classifiers with Indonesian SBERT embeddings achieve the highest F1 score performance. Despite slightly lower performance, this study has proven the language-agnostic capability of LLM2Vec, especially with Llama 3 8B and Mistral 7B in colloquial Bahasa Indonesia sentiment analysis, since none of the base decoders were ever trained using the Bahasa Indonesia corpus. © 2024 IEEE.

关键词： Decoding

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Tag clouds for summarizing web search results 07

Tag clouds for summarizing web search results

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16th International World Wide Web Conference, WWW2007

作者： Kuo, Byron Y.-L. Hentrich, Thomas Good, Benjamin M . Wilkinson, Mark D. ICAPTURE Centre for Cardiovascular and Pulmonary Research University of British Columbia St. Paul.s Hospital Vancouver BC V6Z 1Y6 Canada Computing Science Simon Fraser University Burnaby BC Canada Bioinformatics Graduate Program University of British Columbia Vancouver BC Canada

ISBN: (纸本)1595936548

In this paper, we describe an application, PubCloud that uses tagclouds for the summarization of results from queries over thePubMed database of biomedical literature. PubCloud responds toqueries of this database with tag clouds generated from wordsextracted from the abstracts returned by the query. The results ofa user study comparing the PubCloud tag-cloud summarization ofquery results with the standard result list provided by PubMedindicated that the tag cloud interface is advantageous in presenting descriptive information and in reducing user frustrationbut that it is less effective at the task of enabling users to discoverrelations between concepts.

关键词： Online searching

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An Exploratory Computational Approach for Elucidating a Nonstructural Protein Interaction in Dengue Virus 2 9th

An Exploratory Computational Approach for Elucidating a Nons...

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9th International Conference on Computer Science and Computational Intelligence, ICCSCI 2024

作者： Hidayat, Alam Ahmad Nirwantono, Rudi Pardamean, Bens Mathematics Department School of Computer Science Bina Nusantara University 11480 Indonesia Biotechnology Department Faculty of Engineering Bina Nusantara University 11480 Indonesia Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta11480 Indonesia Computer Science Department BINUS Graduate Program Bina Nusantara University Jakarta11480 Indonesia

As the dengue infection still impacts hundreds of millions of people globally, unprecedented efforts in dengue drug development have been more progressive in recent decades. Computational methods provide a fast, sustainable, and efficient screening of active compounds and newly created drug molecules, including those specifically targeting nonstructural proteins (NS) of dengue viruses. In this work, protein modeling for the NS proteins of DENV-2/16681 strain was performed using a template-based homology modeling for the NS3 protein and an Artificial Intelligence (AI)-based prediction via AlphaFold for the NS4B protein. Moreover, the protein-protein interaction between the two structures was predicted using the HADDOCK server, which employs information about active and passive residues of the interaction interface to guide the docking process. After the modeling and its respective refinement process, the predicted structures of NS3 and NS4B improved their steric clashing scoring from MolProbity assessment. The refined models were then docked, and the resulting docking pose was analyzed to extract the interacting residues based on the polar contacts within the interface of the two proteins. Our result presents a preliminary study to create a dataset related to in silico molecular interactions of the NS3-NS4B interaction of different DENV types. It is helpful for building a computational pipeline for elucidating protein-ligand problems in dengue drug screenings. © 2024 The Authors.

关键词： Molecular docking

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Structure of the active microbial community in a pilot-scale enhanced biological phosphorus removal process revealed through 454 pyrotag sequencing 86

Structure of the active microbial community in a pilot-scale...

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86th Annual Water Environment Federation Technical Exhibition and Conference, WEFTEC 2013

作者： Lawson, Christopher E. Rabinowitz, Barry Mavinic, Donald S. Ramey, William D. Hallam, Steven J. Department of Civil Engineering University of British Columbia VancouverBC Canada Department of Microbiology and Immunology University of British Columbia VancouverBC Canada Graduate Program in Bioinformatics University of British Columbia VancouverBC Canada CH2M Hill Canada 2100 Metrotower II 4720 Kingsway Suite 2100 BurnabyBC Canada

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