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Understanding and applying biological resilience, from genes to ecosystems

NPJ Biodiversity 2023年第1期2卷 16页

作者： Thorogood, Rose Mustonen, Ville Aleixo, Alexandre Aphalo, Pedro J. Asiegbu, Fred O. Cabeza, Mar Cairns, Johannes Candolin, Ulrika Cardoso, Pedro Eronen, Jussi T. Hällfors, Maria Hovatta, Iiris Juslén, Aino Kovalchuk, Andriy Kulmuni, Jonna Kuula, Liisa Mäkipää, Raisa Ovaskainen, Otso Pesonen, Anu-Katriina Primmer, Craig R. Saastamoinen, Marjo Schulman, Alan H. Schulman, Leif Strona, Giovanni Vanhatalo, Jarno HiLIFE Helsinki Institute of Life Science University of Helsinki Helsinki Finland Research Programme in Organismal & Evolutionary Biology Faculty of Biological and Environmental Sciences University of Helsinki Helsinki Finland Department of Computer Science Faculty of Science University of Helsinki Helsinki Finland Helsinki Institute for Information Technology University of Helsinki Helsinki Finland Institute of Biotechnology HiLIFE Helsinki Institute for Life Science University of Helsinki Helsinki Finland LUOMUS Finnish Museum of Natural History University of Helsinki Helsinki Finland Viikki Plant Science Centre University of Helsinki Helsinki Finland Department of Forest Sciences Faculty of Agriculture and Forestry University of Helsinki Helsinki Finland HELSUS Helsinki Institute of Sustainability Science University of Helsinki Helsinki Finland CE3C - Centre for Ecology Evolution and Environmental Changes CHANGE—Global Change and Sustainability Institute Faculty of Sciences University of Lisbon Lisbon 1749-016 Portugal Research Programme in Ecosystems and Environment Faculty of Biological and Environmental Sciences University of Helsinki Helsinki Finland BIOS Research Unit Helsinki Finland Research Centre for Ecological Change Faculty of Biological and Environmental Sciences University of Helsinki Helsinki Finland Syke Finnish Environment Institute Helsinki Finland SleepWell Research Program Faculty of Medicine University of Helsinki Helsinki Finland Department of Psychology and Logopedics Faculty of Medicine University of Helsinki Helsinki Finland Neuroscience Center HiLIFE Helsinki Institute for Life Science University of Helsinki Helsinki Finland VTT Technical Research Centre of Finland Ltd Espoo Finland Department of Evolutionary and Population Biology Institute for Biodiversity and Ecosystem Dynamics University of Amsterdam Amsterdam Netherlands Natural Resources Institute Finland (Luke) Helsinki Finland Centre for Biodiversity Dynamics

The natural world is under unprecedented and accelerating pressure. Much work on understanding resilience to local and global environmental change has, so far, focussed on ecosystems. However, understanding a system’s behaviour requires knowledge of its component parts and their interactions. Here we call for increased efforts to understand ‘biological resilience’, or the processes that enable components across biological levels, from genes to communities, to resist or recover from perturbations. Although ecologists and evolutionary biologists have the tool-boxes to examine form and function, efforts to integrate this knowledge across biological levels and take advantage of big data (e.g. ecological and genomic) are only just beginning. We argue that combining eco-evolutionary knowledge with ecosystem-level concepts of resilience will provide the mechanistic basis necessary to improve management of human, natural and agricultural ecosystems, and outline some of the challenges in achieving an understanding of biological resilience. © The Author(s) 2023.

关键词： Ecology Biodiversity Community ecology Ecological modelling Ecosystem ecology Evolutionary ecology Molecular ecology Palaeoecology

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BigNeuron: a resource to benchmark and predict performance of algorithms for automated tracing of neurons in light microscopy datasets

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Nature methods 2023年第6期20卷 824-835页

作者： Linus Manubens-Gil Zhi Zhou Hanbo Chen Arvind Ramanathan Xiaoxiao Liu Yufeng Liu Alessandro Bria Todd Gillette Zongcai Ruan Jian Yang Miroslav Radojević Ting Zhao Li Cheng Lei Qu Siqi Liu Kristofer E Bouchard Lin Gu Weidong Cai Shuiwang Ji Badrinath Roysam Ching-Wei Wang Hongchuan Yu Amos Sironi Daniel Maxim Iascone Jie Zhou Erhan Bas Eduardo Conde-Sousa Paulo Aguiar Xiang Li Yujie Li Sumit Nanda Yuan Wang Leila Muresan Pascal Fua Bing Ye Hai-Yan He Jochen F Staiger Manuel Peter Daniel N Cox Michel Simonneau Marcel Oberlaender Gregory Jefferis Kei Ito Paloma Gonzalez-Bellido Jinhyun Kim Edwin Rubel Hollis T Cline Hongkui Zeng Aljoscha Nern Ann-Shyn Chiang Jianhua Yao Jane Roskams Rick Livesey Janine Stevens Tianming Liu Chinh Dang Yike Guo Ning Zhong Georgia Tourassi Sean Hill Michael Hawrylycz Christof Koch Erik Meijering Giorgio A Ascoli Hanchuan Peng Institute for Brain and Intelligence Southeast University Nanjing China. Microsoft Corporation Redmond WA USA. Tencent AI Lab Bellevue WA USA. Computing Environment and Life Sciences Directorate Argonne National Laboratory Lemont IL USA. Kaya Medical Seattle WA USA. University of Cassino and Southern Lazio Cassino Italy. Center for Neural Informatics Structures and Plasticity Krasnow Institute for Advanced Study George Mason University Fairfax VA USA. Faculty of Information Technology Beijing University of Technology Beijing China. Beijing International Collaboration Base on Brain Informatics and Wisdom Services Beijing China. Nuctech Netherlands Rotterdam the Netherlands. Janelia Research Campus Howard Hughes Medical Institute Ashburn VA USA. Department of Electrical and Computer Engineering University of Alberta Edmonton Alberta Canada. Ministry of Education Key Laboratory of Intelligent Computation and Signal Processing Anhui University Hefei China. Paige AI New York NY USA. Scientific Data Division and Biological Systems and Engineering Division Lawrence Berkeley National Lab Berkeley CA USA. Helen Wills Neuroscience Institute and Redwood Center for Theoretical Neuroscience UC Berkeley Berkeley CA USA. RIKEN AIP Tokyo Japan. Research Center for Advanced Science and Technology (RCAST) The University of Tokyo Tokyo Japan. School of Computer Science University of Sydney Sydney New South Wales Australia. Texas A&M University College Station TX USA. Cullen College of Engineering University of Houston Houston TX USA. Graduate Institute of Biomedical Engineering National Taiwan University of Science and Technology Taipei Taiwan. National Centre for Computer Animation Bournemouth University Poole UK. PROPHESEE Paris France. Department of Neuroscience Columbia University New York NY USA. Mortimer B. Zuckerman Mind Brain Behavior Institute Columbia University New York NY USA. Department of Computer Science Northern Illinois Universit

BigNeuron is an open community bench-testing platform with the goal of setting open standards for accurate and fast automatic neuron tracing. We gathered a diverse set of image volumes across several species that is representative of the data obtained in many neuroscience laboratories interested in neuron tracing. Here, we report generated gold standard manual annotations for a subset of the available imaging datasets and quantified tracing quality for 35 automatic tracing algorithms. The goal of generating such a hand-curated diverse dataset is to advance the development of tracing algorithms and enable generalizable benchmarking. Together with image quality features, we pooled the data in an interactive web application that enables users and developers to perform principal component analysis, t-distributed stochastic neighbor embedding, correlation and clustering, visualization of imaging and tracing data, and benchmarking of automatic tracing algorithms in user-defined data subsets. The image quality metrics explain most of the variance in the data, followed by neuromorphological features related to neuron size. We observed that diverse algorithms can provide complementary information to obtain accurate results and developed a method to iteratively combine methods and generate consensus reconstructions. The consensus trees obtained provide estimates of the neuron structure ground truth that typically outperform single algorithms in noisy datasets. However, specific algorithms may outperform the consensus tree strategy in specific imaging conditions. Finally, to aid users in predicting the most accurate automatic tracing results without manual annotations for comparison, we used support vector machine regression to predict reconstruction quality given an image volume and a set of automatic tracings.

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Resource-optimized fermionic local-hamiltonian simulation on a quantum computer for quantum chemistry

arXiv

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arXiv 2020年

作者： Wang, Qingfeng Li, Ming Monroe, Christopher Nam, Yunseong Chemical Physics Program Institute for Physical Science and Technology University of Maryland College ParkMD20742 United States IonQ College ParkMD20740 United States Joint Quantum Institute Department of Physics Joint Center for Quantum Information and Computer Science University of Maryland College ParkMD20742 United States Department of Physics University of Maryland College ParkMD20742 United States

The ability to simulate a fermionic system on a quantum computer is expected to revolutionize chemical engineering, materials design, nuclear physics, to name a few. Thus, optimizing the simulation circuits is of significance in harnessing the power of quantum computers. Here, we address this problem in two aspects. In the fault-tolerant regime, we optimize the rz and t gate counts along with the ancilla qubit counts required, assuming the use of a product-formula algorithm for implementation. We obtain a savings ratio of two in the gate counts and a savings ratio of eleven in the number of ancilla qubits required over the state of the art. In the pre-fault tolerant regime, we optimize the two-qubit gate counts, assuming the use of the variational quantum eigensolver (VQE) approach. Specific to the latter, we present a framework that enables bootstrapping the VQE progression towards the convergence of the ground-state energy of the fermionic system. This framework, based on perturbation theory, is capable of improving the energy estimate at each cycle of the VQE progression, by about a factor of three closer to the known ground-state energy compared to the standard VQE approach in the test-bed, classically-accessible system of the water molecule. The improved energy estimate in turn results in a commensurate level of savings of quantum resources, such as the number of qubits and quantum gates, required to be within a pre-specified tolerance from the known ground-state energy. We also explore a suite of generalized transformations of fermion to qubit operators and show that resource-requirement savings of up to more than 20%, in small instances, is possible. © 2020, CC BY.

关键词： Fault tolerance

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Evaluation of PHP Framework Measured Using Object-Oriented Metrics with the Analytic Hierarchy Process

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IOP Conference Series: Materials science and Engineering 2020年第1期874卷

作者： R Setiyawan W Gata Elbiansyah D Ardiansyah D Yuliandari D Wijayanti F P Harmono Y Komalasari M Lase M H Fakhriza Master of Computer Science Postgraduate Program STMIK Nusa Mandiri Indonesia Information System Universitas Bina Sarana Informatika Indonesia Information Technology Universitas Bina Sarana Informatika Indonesia Information Technology Postgraduate Program STMIK Nusa Mandiri Indonesia

The existence of various PHP frameworks may become one alternative choice in developing a web application that PT XYZ wants to evaluate its Wisanggeni internal PHP framework in order to measure how far the design quality of Wisanggeni framework is working. An evaluation on PHP framework using object-oriented metric parameter and design quality is then conducted in this research. The results of measurement conducted using object-oriented metric parameters for each framework are evaluated with the Analytic Hierarchy Process (AHP) method to determine the best framework model design quality used as a reference for the development of Wisanggeni. This study also uses a combination of PHPDepend and PHPMetrics devices to measure the values of object-oriented metrics in each PHP framework. The research final result is that each framework has one value representing each framework's quality in which the quality of Wisanggeni framework is almost to the same with the Laravel and CodeIgniter framework.

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The Application of AGNES Algorithm to Optimize Knowledge Base for Tourism Chatbot 3

The Application of AGNES Algorithm to Optimize Knowledge Bas...

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3rd International Conference on information Management and technology, ICIMTech 2018

作者： Sano, Albert Verasius Dian Imanuel, Tanto Daud Intanadias Calista, Mega Nindito, Hendro Condrobimo, Andreas Raharto Bina Nusantara Institute of Creative Technology Computer Science Study Program Malang65126 Indonesia Information Systems Department School of Information Systems Bina Nusantara University Jakarta11480 Indonesia

ISBN: (纸本)9781538658215

Most tourists have limited time and schedule when they are visiting a particular tourism area. One of the main issues faced by those tourists is that they can not make simple queries to search engines about, for example, which sites or places to visit optimally if we only have one day or two-day visit? Search engines are better and better in replying users' queries with relevant answers. However, search engines are not always able to respond queries suited to users' characteristics such as their styles, personalities, knowledge backgrounds, etc. Also, search engines are not as flexible as chatbots in enabling dialogical-communication-queries. This case study aims to respond aformentioned issue by applying hierarchical cluster analysis on a set of tourism sites around Malang city, Malang regency, and Batu city based on AGNES (Agglomerative Nesting) algorithm. The result, then, is fed into chatbot's knowledge base. This chatbot will assist tourists to get information on which possible sites they have to visit optimally if they are under limited vacancy-Time constraints. © 2018 IEEE.

关键词： Search engines

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Service Quality Improvement by Using the Quality Function Deployment (QFD) Method at the Government General Hospital 1

Service Quality Improvement by Using the Quality Function De...

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1st Workshop on Environmental science, Society, and technology, WESTECH 2018

作者： Hasibuan, Abdurrozzaq Parinduri, Luthfi Sulaiman, Oris Krianto Suleman, Abdul Rahman Harahap, Adek Khadijatul Z Hasibuan, Masnilam Rupilele, Frits Gerit John Simarmata, Janner Kurniasih, Nuning Achmad Daengs, G.S. Abdussakir Faculty of Engineering Universitas Islam Sumatera Utara Medan Indonesia Faculty of Computer Science Universitas Victory Sorong Sorong Indonesia Faculty of Economic Universitas Graha Nusantara Padangsidimpuan Indonesia Universitas Negeri Medan Medan Indonesia Faculty of Communication Sciences Library and Information Science Program Universitas Padjadjaran Bandung Indonesia Faculty of Economic Universitas 45 Surabaya Surabaya Indonesia Faculty of Science and Technology Universitas Islam Negeri Maulana Malik Ibrahim Malang Indonesia

In the face of increasingly competitive competition in the hospital industry, RSU managers are required to be able to develop strategies, policies or new breakthroughs related to improving the quality of their services, through improving the characteristics of hospital services, which focus on patient needs, so that the risk of errors or discrepancies between service characteristics that are enhanced by what the patient wants can be avoided or minimized. From the results of research conducted there are 21 variables of patient needs from a health service at the Government General Hospital (RSU). Whereas the patient's research on the service quality of the Government Hospital is 1 variable that has fulfilled the needs of patients, namely that they are satisfied with the quality of hospital services. Variable is the state and completeness of modern medical facilities. Whereas for other variables there are gaps so that they cannot meet patient expectations until the highest quality limit is very satisfied, it is necessary to have a direction of improvement. To obtain the suitability, the technique used to improve the characteristics of the service is the application of the QFD method. The QFD method in this study is in the form of a quality service matrix at the Government General Hospital. From the HOQ matrix, the service quality of the Government Hospital is obtained from the input of the Government Hospital/management that there are priority variables needed to improve their quality, which is generally the patient's needs related to the recovery of patients, including the knowledge and abilities of doctors, medicines the treatment given in the healing of patients, the service of examination, treatment and care that is fast and precise, guarantee of security and trust in the services provided and the completeness of the readiness and cleanliness of the equipment used. So there are 33 service quality characteristics prioritized for further improvement, with the main pr

关键词： Quality function deployment

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Web Security and Vulnerability: A Literature Review

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Journal of Physics: Conference Series 2020年第2期1477卷

作者： H Yulianton H L H S Warnars B Soewito F L Gaol E Abdurachman Computer Science Department BINUS Graduate Program - Doctor of Computer Science Bina Nusantara University Jakarta Indonesia 11480 Faculty of Information Technology Universitas Stikubank Semarang Indonesia 50243

The web continues to grow and attacks against the web continue to increase. This paper focuses on the literature review on scanning web vulnerabilities and solutions to mitigate web attacks. Vulnerability scanning methods will be reviewed as well as frameworks for improving web security. This research is the basis for future work that will end with the elaboration of web scanning and security with the aim of proposing better innovations.

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Perceptron Partition Model to Minimize Input Matrix

Perceptron Partition Model to Minimize Input Matrix

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International Conference on science and Innovated Engineering 2018, i-COSINE 2018

作者： Azmi, Zulfian Nasution, Mahyuddin K.M. Zarlis, Muhammad. Mawengkang, Herman Efendi, Syahril Postgraduate Doctoral of Computer Science Universitas Sumatera Utara Padang Bulan USU Medan20155 Indonesia Information Technology Department Universitas Sumatera Utara Padang Bulan USU Medan20155 Indonesia Program Pasca Sarjana Doktoral Ilmu Komputer Universitas Sumatera Utara Indonesia Department of Mathematics Universitas Sumatera Utara Padang BulanUSU Medan20155 Indonesia

Implementation of Neuron Network model using Perceptron has not given optimal result in real time learning. The large number of inputs expressed in matrix form makes the process slower in pattern recognition. So, it takes characteristic to represent all the input matrices by using the partition method. By partitioning each input and with the best weight and using the activation function will produce an output value. And learning is valid in recognizing patterns only 1 iteration only. Further validation is done on the water mill control module with dissolved oxygen input, water pH, salinity and water temperature. With Perceptron Partition learning algorithm more real-time than perceptron model. Testing on the waterwheel input whether rotating or stopping by Matrix Laboratory software simulation. © Published under licence by IOP Publishing Ltd.

关键词： Neural networks

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Airr Community Curation and Standardised Representation for Immunoglobulin and T Cell Receptor Germline Sets

SSRN

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SSRN 2022年

作者： Lees, William D. Christley, Scott Peres, Ayelet Kos, Justin T. Corrie, Brian Ralph, Duncan Breden, Felix Cowell, Lindsay G. Yaari, Gur Corcoran, Martin Karlsson Hedestam, Gunilla B. Ohlin, Mats Collins, Andrew M. Watson, Corey T. Busse, Christian E. Institute of Structural and Molecular Biology Birkbeck College London United Kingdom Human-Centered Computing and Information Science Institute for Systems and Computer Engineering Technology and Science Porto Portugal Peter O’Donnell Jr School of Public Health Department of Immunology UT Southwestern Medical Center Texas United States Bioengineering Program Faculty of Engineering Bar-Ilan University Ramat Gan Israel Department of Biochemistry and Molecular Genetics School of Medicine University of Louisville Kentucky United States Department of Biological Sciences Simon Fraser University BurnabyBC Canada Fred Hutchinson Cancer Research Center SeattleWA United States Department of Microbiology Tumor and Cell Biology Karolinska Institute Stockholm Sweden Department of Immunotechnology Lund University Lund Sweden School of Biotechnology and Biomolecular Sciences University of New South Wales SydneyNSW Australia Division of B Cell Immunology German Cancer Research Center Heidelberg Germany

Analysis of an individual’s immunoglobulin or T cell receptor gene repertoire can provide important insights into immune function. High-quality analysis of adaptive immune receptor repertoire sequencing data depends upon accurate and relatively complete germline sets, but current sets are known to be incomplete. Established processes for the review and systematic naming of receptor germline genes and alleles require specific evidence and data types, but the discovery landscape is rapidly changing. To exploit the potential of emerging data, and to provide the field with improved state-of-the-art germline sets, an intermediate approach is needed that will allow the rapid publication of consolidated sets derived from these emerging sources. These sets must use a consistent naming scheme and allow refinement and consolidation into genes as new information emerges. Name changes should be minimised, but, where changes occur, the naming history of a sequence must be traceable. Here we outline the current issues and opportunities for the curation of germline IG/TR genes and present a forward-looking data model for building out more robust germline sets that can dovetail with current established processes and provides transparency based on principles of findability, accessibility, interoperability, and reusability. We describe results obtained by applying the data model and associated principles within the AIRR Community, including supporting software and databases. © 2022, The Authors. All rights reserved.

关键词： Genes

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Implementation of Mobile game for Religion Learning

Implementation of Mobile game for Religion Learning

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IEEE International Conference on Teaching, Assessment and Learning for Engineering (TALE)

作者： Edy Sulistiyo Vindy Nizirwan Anwar Diana Teresia Spits Warnars Setya Chendra Wibawa Goenawan Brotosaputro Dedy Prasetya Kristiadi Harco Leslie Hendric Spits Warnars Kiyota Hashimoto Electrical Engineering Department Universitas Negeri Surabaya Jawa Timur Indonesia Game Application & Technology Program School of Computer Science Bina Nusantara University Jakarta Indonesia Faculty of Computer Science Esa Unggul University Jakarta Indonesia Information Systems Department Bina Nusantara University Jakarta Indonesia Informatics Department Universitas Negeri Surabaya Jawa Timur Indonesia Information System Department Universitas Budi Luhur Jakarta Indonesia Computer Science department Raharja University Tangerang Indonesia Computer Science Department BINUS Graduate Program – Doctor of Computer Science Bina Nusantara University Jakarta Indonesia Faculty of Technology and Environment Prince Songkla University Phuket Campus Thailand

ISBN: (数字)9781728126654

ISBN: (纸本)9781728126661

Currently, the growth of information and technology is rapid. It makes a lot of things in various fields including education becoming more effective and efficient. In education, one of its implementation which is a game is proven to be a useful tool to support conventional teaching methods and bring a more natural understanding of learning materials. Moreover, as a product of the popular culture in modern society, video game mirrors the general culture practice in real life and reflects it via its own culture inside the game. This makes a video game can give a contribution to the social construction of reality as it affects the player's view towards learning in real life and vice versa. From there, we see that there is an opportunity for learning about religion to be supported by its utilization to provide an interactive and fun learning experience. In this paper, we discuss how a video game is implemented to support religious learning. The game was developed with the scrum method where we surveyed to gather the user requirements before the design step. The game design was made by using the use case diagram and storyboard, and it was built using Unity version 2017.3.0f3.

关键词： Games Land mobile radio Education computer science Operating systems information systems Media

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