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26th International Conference on Research in Computational Molecular Biology, RECOMB 2022

作者： Rachtman, Eleonora Sarmashghi, Shahab Bafna, Vineet Mirarab, Siavash Bioinformatics and Systems Biology Graduate Program UC San Diego La JollaCA United States Department of Electrical and Computer Engineering UC San Diego La JollaCA United States Department of Computer Science and Engineering UC San Diego La JollaCA United States

Computing the distance between two genomes, often without using alignments or even access to assembled sequences, is fundamental to many downstream analyses. © 2022, The Author(s), under exclusive license to Spri... 详细信息

ISBN: (纸本)9783031047480

关键词： Uncertainty analysis

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Neuronal aging causes mislocalization of splicing proteins and unchecked cellular stress

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Nature neuroscience 2025年 2025 Jun 2页

作者： Kevin Rhine Rachel Li Hema M Kopalle Katherine Rothamel Xuezhen Ge Elle Epstein Orel Mizrahi Assael A Madrigal Hsuan-Lin Her Trent A Gomberg Anita Hermann Joshua L Schwartz Amanda J Daniels Uri Manor John Ravits Robert A J Signer Eric J Bennett Gene W Yeo Department of Cellular & Molecular Medicine University of California San Diego La Jolla CA USA. Sanford Stem Cell Institute Innovation Center and Sanford Consortium for Regenerative Medicine University of California San Diego La Jolla CA USA. Institute for Genomic Medicine University of California San Diego La Jolla CA USA. Waitt Advanced Biophotonics Center Salk Institute for Biological Studies La Jolla CA USA. Biomedical Sciences Graduate Program University of California San Diego La Jolla CA USA. Biological Sciences Graduate Program University of California San Diego La Jolla CA USA. Center for RNA Technologies & Therapeutics University of California San Diego La Jolla CA USA. Department of Cell & Developmental Biology University of California San Diego La Jolla CA USA. Bioinformatics & Systems Biology Graduate Program University of California San Diego La Jolla CA USA. Department of Neurosciences School of Medicine University of California San Diego La Jolla CA USA. Division of Regenerative Medicine Department of Medicine Sanford Stem Cell Institute Moores Cancer Center University of California San Diego La Jolla CA USA. Department of Cellular & Molecular Medicine University of California San Diego La Jolla CA USA. geneyeo@ucsd.edu. Sanford Stem Cell Institute Innovation Center and Sanford Consortium for Regenerative Medicine University of California San Diego La Jolla CA USA. geneyeo@ucsd.edu. Institute for Genomic Medicine University of California San Diego La Jolla CA USA. geneyeo@ucsd.edu. Biomedical Sciences Graduate Program University of California San Diego La Jolla CA USA. geneyeo@ucsd.edu. Biological Sciences Graduate Program University of California San Diego La Jolla CA USA. geneyeo@ucsd.edu. Center for RNA Technologies & Therapeutics University of California San Diego La Jolla CA USA. geneyeo@ucsd.edu. Bioinformatics & Systems Biology Graduate Program University of California San Diego La Jolla CA USA. geneyeo@ucsd.edu.

Aging is one of the most prominent risk factors for neurodegeneration, yet the molecular mechanisms underlying the deterioration of old neurons are mostly unknown. To efficiently study neurodegeneration in the context of aging, we transdifferentiated primary human fibroblasts from aged healthy donors directly into neurons, which retained their aging hallmarks, and we verified key findings in aged human and mouse brain tissue. Here we show that aged neurons are broadly depleted of RNA-binding proteins, especially spliceosome components. Intriguingly, splicing proteins-like the dementia- and ALS-associated protein TDP-43-mislocalize to the cytoplasm in aged neurons, which leads to widespread alternative splicing. Cytoplasmic spliceosome components are typically recruited to stress granules, but aged neurons suffer from chronic cellular stress that prevents this sequestration. We link chronic stress to the malfunctioning ubiquitylation machinery, poor HSP90α chaperone activity and the failure to respond to new stress events. Together, our data demonstrate that aging-linked deterioration of RNA biology is a key driver of poor resiliency in aged neurons.

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Twitter-based text classification using svm for weather information system 6

Twitter-based text classification using svm for weather info...

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6th International Conference on Information Management and Technology, ICIMTech 2021

作者： Purwandari, Kartika Rahutomo, Reza Sigalingging, Join W. C. Ajy Kusuma, Mahisa Prasetyo, Aji Pardamean, Bens Research Center Bina Nusantara University Bioinformatics and Data Science Jakarta11480 Indonesia BMKG Meteorological Climatological and Geophysical Agency Database Center Division Jakarta10720 Indonesia Bina Nusantara University BINUS Graduate Program - Master of Computer Science Computer Science Department Jakarta11480 Indonesia

ISBN: (纸本)9781665449373

The popularity of social media amplified the amount of text data that is used to enrich text classification research with machine learning approach. The modernization in weather information system is needed to produce real-time weather information using the involvement of Twitter users. GetOldTweets was used to cover data acquisition from Twitter. Support Vector Machine (SVM) was deployed as a machine learning model for text classification. The result was delivered in Esri Maps features. It facilitated a social sensing for Indonesia weather information system by using Twitter posts from Indonesian users with 93% accuracy. © 2021 IEEE.

关键词： Data acquisition

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Simulation of developmental changes in action potentials with ventricular cell models

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Systems and Synthetic Biology 2007年第1期1卷 11-23页

作者： Itoh, Hitomi Naito, Yasuhiro Tomita, Masaru Institute for Advanced Biosciences Keio University Fujisawa Kanagawa 252-8520 Japan Bioinformatics Program Graduate School of Media and Governance Keio University Fujisawa Kanagawa 252-8520 Japan Japan Society for the Promotion of Science (DC1) Tokyo Japan Department of Environmental Information Keio University Fujisawa Kanagawa 252-8520 Japan

During cardiomyocyte development, early embryonic ventricular cells show spontaneous activity that disappears at a later stage. Dramatic changes in action potential are mediated by developmental changes in individual ionic currents. Hence, reconstruction of the individual ionic currents into an integrated mathematical model would lead to a better understanding of cardiomyocyte development. To simulate the action potential of the rodent ventricular cell at three representative developmental stages, quantitative changes in the ionic currents, pumps, exchangers, and sarcoplasmic reticulum (SR) Ca²⁺ kinetics were represented as relative activities, which were multiplied by conductance or conversion factors for individual ionic systems. The simulated action potential of the early embryonic ventricular cell model exhibited spontaneous activity, which ceased in the simulated action potential of the late embryonic and neonatal ventricular cell models. The simulations with our models were able to reproduce action potentials that were consistent with the reported characteristics of the cells in vitro. The action potential of rodent ventricular cells at different developmental stages can be reproduced with common sets of mathematical equations by multiplying conductance or conversion factors for ionic currents, pumps, exchangers, and SR Ca ²⁺ kinetics by relative activities. © Springer Science + Business Media B.V. 2007.

关键词： Cardiac ventricular cell Computer modeling Development Electrophysiology Ion channels Spontaneous electrical activity

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Pinned, locked, pushed, and pulled traveling waves in structured environments

arXiv

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arXiv 2018年

作者： Wang, Ching-Hao Matin, Sakib George, Ashish B. Korolev, Kirill S. Department of Physics Boston University BostonMA02215 United States Department of Physics and Graduate Program in Bioinformatics Boston University BostonMA02215

Traveling fronts describe the transition between two alternative states in a great number of physical and biological systems. Examples include the spread of beneficial mutations, chemical reactions, and the invasions by foreign species. In homogeneous environments, the alternative states are separated by a smooth front moving at a constant velocity. This simple picture can break down in structured environments such as tissues, patchy landscapes, and microfluidic devices. Habitat fragmentation can pin the front at a particular location or lock invasion velocities into specific values. Locked velocities are not sensitive to moderate changes in dispersal or growth and are determined by the spatial and temporal periodicity of the environment. The synchronization with the environment results in discontinuous fronts that propagate as periodic pulses. We characterize the transition from continuous to locked invasions and show that it is controlled by positive density-dependence in dispersal or growth. We also demonstrate that velocity locking is robust to demographic and environmental fluctuations and examine stochastic dynamics and evolution in locked invasions. Copyright © 2018, The Authors. All rights reserved.

关键词： Velocity

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A Design of Childhood Stunting Assessment Feature with Agile UX Approach 8

A Design of Childhood Stunting Assessment Feature with Agile...

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8th International HCI and UX Conference in Indonesia, CHIuXiD 2022

作者： Rahutomo, Reza Perbangsa, Anzaludin Samsinga Asadi, Faisal Nirwantono, Rudi Pardamean, Bens Bina Nusantara University School of Information Systems Information Systems Department Jakarta11480 Indonesia Bina Nusantara University Bioinformatics and Data Science Research Center Jakarta11480 Indonesia Bina Nusantara University BINUS Graduate Program-Master of Computer Science Computer Science Department Jakarta11480 Indonesia

ISBN: (纸本)9781665476645

multidisciplinary collaboration between public health, system engineering, and UX is able to generate a solution in healthcare problem like stunting. The principle of Agile UX gathers requirements to generate an application design. Currently, various website and mobile applications are available to be utilized for stunting research. StuntingDB is one of many web-based applications that specialized in stunting data management. The application required several types of users to operate hierarchically. This research focused on Public Health Officers' workflow that require a solution to in the form of assessment module for stunting DBMS by using Agile UX principle. The method collaborates agile team and UX team to solve Public Health Officer's difficulty in changing stunting status at pre-saved child patient's profile. Collaboration of both agile team and UX team successfully proposed an application design that system design. © 2022 IEEE.

关键词： Websites

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Identification of Meteorological Parameters Affecting Dengue Hemorrhagic Fever Incidences 4

Identification of Meteorological Parameters Affecting Dengue...

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4th International Conference on Informatics, Multimedia, Cyber and Information System, ICIMCIS 2022

作者： Asadi, Faisal Trinugroho, Joko Pebrianto Hidayat, Alam Ahmad Rahutomo, Reza Pardamean, Bens Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta11480 Indonesia School of Information Systems Bina Nusantara University Information System Department Jakarta11480 Indonesia Binus Graduate Program Master of Computer Science Bina Nusantara University Computer Science Department Jakarta11480 Indonesia

ISBN: (纸本)9781665473279

Tropical disease is one of the infectious diseases that affect Indonesia. Many people die because of tropical diseases, such as dengue hemorrhagic fever (DHF), chikungunya, leprosy, lymphatic, and filariasis. The Indonesian government's lack of public policy is the main problem in treating and preventing tropical diseases. The paper aims to describe the analysis results of the incidence of DHF in Jakarta, Indonesia. The analysis used the DHF incidences data from the Jakarta Health service surveillance office representative and combined it with the meteorological parameters data. The meteorological parameters were collected from the Bureau of Meteorological Climatology and Geophysics (BMKG). The statistical analysis of this research used Pearson's correlation. The results show that the meteorological parameters affecting DHF incidences are temperature, humidity, and wind speed. © 2022 IEEE.

关键词： Correlation methods

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Systematic Literature Review on Statistics and Machine Learning Predictive Models for Rice Phenotypes 8

Systematic Literature Review on Statistics and Machine Learn...

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8th International Conference on Computer Science and Computational Intelligence, ICCSCI 2023

作者： Dominic, Nicholas Cenggoro, Tjeng Wawan 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 Computer Science Department BINUS Graduate Program - Master of Computer Science Bina Nusantara University Jakarta11480 Indonesia

Predicting the best-quality of rice phenotypes is the priority among agricultural researchers to fulfill worldwide food security. Trend development of predictive models from statistics to machine learning is the subject of this review. Gathered from the Google Scholar database, 14 appropriate papers (2016-2020) related to the rice phenotypes prediction were selected through title and abstract content filtering. The outputs show that Support Vector Machine, Multi-layer Perceptron, and regression are the most used models, while yield is the priority prediction point besides tiller, panicle, and 1000-grain weight of rice. However, finding the accurate predictor is invariably challenging due to distinct rice varieties in the world and high confounding factors. Thus, developing an advanced deep learning model that accommodates these needs is worth considering further. © 2023 The Authors. Published by Elsevier B.V.

关键词： machine learning rice phenotypes prediction statistics

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Lockdown strategy worth lives: The SEIRD modelling in COVID-19 outbreak in Indonesia 2

Lockdown strategy worth lives: The SEIRD modelling in COVID-...

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2nd International Conference on Biospheric Harmony Advanced Research, ICOBAR 2020

作者： Nurlaila, I. Hidayat, A.A. Pardamean, B. Information Systems Department BINUS Online Learning Bina Nusantara University Jakarta11480 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

Lockdowns, despite their conflicting restrictions and consequences they might offer when enforced as a national strategy, are deemed to be suggestive for a prompt conquer to the Coronavirus Disease-19 (COVID-19) outbreak. There have been some success stories such as in China, South Korea and our ASEAN member fellow, Vietnam, which exhibited extremely fallen numbers of COVID-19 cases post the enforcement of lockdown. Indonesia, however, remains in the crux of dispute whether or not the lockdown is opted to force COVID-19 transmission down under control. We, in this respect, employ the most popular model which has been broadly applied in the field of epidemiology, referred to as SEIRD (Susceptible, Exposed, Infectious, Recovered, and Death), the extension form of an age-structured SEIR, where the Death (D) is included to provide more factual situation. We modify the I (Infectious) fraction as symp-tomatic (Is) and asymptomatic (Ia) infectives. There are three lockdown scenarios simulated in our modified SEIRD with the starting date are 26 April 2020 when the immediate lockdown was enacted-and a-week and two-week-gaps, respectively. We figured out that by stipulating the lockdown without delay (26 April 2020), the new cases could be kept below 10,000. A week delay escalates case number to 5,000 and delay for one more week results in beyond 20,000 new cases. Furthermore, when the intervention is delayed following the delayed lockdown, normalization would demand a longer period within which dealing with more critical and dying patients is unavoidable and should be more anticipated. © Published under licence by IOP Publishing Ltd.

关键词： Coronavirus

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Repurposing transfer learning strategy of computer vision for owl sound classification 7

Repurposing transfer learning strategy of computer vision fo...

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7th International Conference on Computer Science and Computational Intelligence, CSCI 2022

作者： Gunawan, Kevin William Hidayat, Alam Ahmad Cenggoro, Tjeng Wawan Pardamean, Bens Computer Science Department BINUS Graduate Program-Master of Computer Science Bina Nusantara University Jakarta11480 Indonesia Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta11480 Indonesia Computer Science Department School of Computer Science Bina Nusantara University Jakarta11480 Indonesia

Accurately predicting an owl species based on its sound can be helpful for owl conservation. To build an accurate model for owl sound classification, deep learning is currently the most preferred algorithm, due to its excellent performance for modeling audio data. However, deep learning is generally underperformed for a small dataset, which is the case for recognizing scops owl sound. To overcome the issue, we proposed a transfer learning strategy, which is common for computer vision tasks, that can alleviate overfitting in a deep learning model for the owl sound classification. In our approach, we propose a neural network architecture consisting of the backbone of a EfficientNet model pre-Trained on the massive ImageNet database. The model takes the sound input that has been converted as two image representations: Spectrogram and Mel Frequency Cepstral Coefficients. Our strategy enables the use of a relatively small size of pre-Trained image classification model, which is widely available, for transfer learning in owl sound classification. Deploying the lightweight model in an automatic sound classifier provides a fast and accurate tool for various owl conservation purposes. © 2022 Elsevier B.V.. All rights reserved.

关键词： Deep learning

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