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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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Learning from the settlement in Mount Merapi’s slopes: Orientation and shape of traditional house

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AIP Conference Proceedings 2017年第1期1818卷

作者： Wiwit Setyowati 1Architecture Study Program Universitas Negeri Semarang Indonesia

Settlement in Mount Merapi’s slopes possesses a strong local wisdom. The purpose of this study was to look for Local Wisdom reflected on the orientation, and shape of the house in Pelemsari Village that location in the highest settlement in Mount Merapi’s slopes. This research was investigated using qualitative-naturalistic approach. The results of the study showed that the house has madhep ngarep orientation which is meant facing the palace. Additionally, it also affirms to the public perception that the orientation of the house is do not dare facing the mountain. The closet is oriented to avoid facing the Qiblah. The orientation of omah bajang is facing south, so when giving offerings, the giver of offerings will be facing mountain. There are two shapes of a house namely omah sinom (wedok roof house) and omah kampung (lanang roof house). In the placement, the omah kampung is placed behind omah sinom, which has a meaning men allow women to sit on their laps so that the wives have a longer lifespan.

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Redesigning the Traditional Food Kiosk Based on Local Knowledge, Case study: Siwalankerto District

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Procedia - Social and Behavioral Sciences 2016年 227卷 560-567页

作者： Gunawan Tanuwidjaja Albert Edwin Wiyono Ardhian Wibowo Gregorius Gerry Lia Margareta Shinata Ridwan Raynaldo Architecture Program Study Petra Christian University Jl. Siwalankerto 121-131 60236 Surabaya Indonesia Students of Architecture Program Study Petra Christian University Jl. Siwalankerto 121-131 60236 Surabaya Indonesia

Siwalankerto Sub-District in Surabaya. Siwalankerto was developed rapidly, influenced by educational facilities development. This further created a demand for sustainable food markets/ food kiosk. On the other hand, the unregulated development of traditional food hawkers along the Siwalankerto road existed. Therefore, architecture program study, Petra University proposed a redesigning strategy for the food kiosks in Siwalankerto Sub-district. The strategy not only would provide healthy-affordable foods for all Siwalankerto's residents, but also would generate income for residents with entrepreneurship and culinary skills. The literatures reviews on sustainable neighborhood, commercial provision, food production and inclusive design were conducted. Furthermore, observations and interviews were conducted to meatball-selling restaurant and food hawker. Secondly, the locational analysis was conducted to determine possible food kioks. Additionally, the participatory design was conducted based on inclusive design principles. The seven (7) food kiosk would be proposed for Siwalankerto. The designs would be developed from a typology of food kiosk design (3m-by-3m module). The food kiosk was designed considering the person with disability, such as: wheel chair users, crutch users and persons with vision disability. On the other hand, the layout were designed with proper kitchen and accessible toilet design. Lastly, the culture exploration could also enriched the functional design such as the food kiosk.

关键词： Sustainable and affordable food stall local material.

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Green Infrastructure Concept for JABODETABEKJUR Metropolitan Area

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IOP Conference Series: Earth and Environmental Science 2017年第1期79卷

作者： Gunawan Tanuwidjaja Bill Gates Chang Architecture Program Study Petra Christian University Jl Siwalankerto 121-131 Surabaya Indonesia Student of Architecture Program Study Petra Christian University Jl Siwalankerto 121-131 Surabaya Indonesia

Sixty 'Mega Cities' would emerge by 2015 catering of 600 million populations, and were threatened by the climate change, because of cyclones, flooding, etc. Jakarta became a metro region covering Jakarta, Bogor, Tangerang, Bekasi, Depok and Cianjur. Jakarta metropolitan faced the very high population growth, urban sprawling, traffic jams, flooding, green open space reduction, environmental degradation, urban slums and illegal street hawkers. Flooding and traffic congestions were the two most important issues to solve. SWOT analysis and urban design solutions were produced to create a sustainable solution. Related to transportation issues, Singapore Mass Rapid Transport (MRT) concept was evaluated. Meanwhile the Netherlands' polder concept as well as Singapore's Integrated Water Management were also analyzed. The development of above ground MRT as well as Busway could be developed to connect Jakarta Metropolitan Region. The networks were developed on the main toll road networks. The MRT and Busway would eventually replace the need of automobile use in the future. The Transit – Oriented – Development (TOD) with high density can be suggested to be concentrated nearby the MRT and Busway interchange stations. The Netherlands' polder and were adopted for urban' low-lying lands in Jakarta Metropolitan Region, A polder system was defined as the Integrated Man-made Drainage System consisting Dikes, Drains, Retention Ponds, Outfall Structures or Pumping Stations. The polder system was proposed to be extended to Tangerang and Bekasi area.

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Landscape Potential Analysis for Ecotourism Destination in the Resort Ii Salak Mountain, Halimun-Salak National Park

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IOP Conference Series: Earth and Environmental Science 2017年第1期91卷

作者： A Kusumoarto A Gunawan G R Nurazizah Lecturer in Study Program of Architecture Faculty of Technology Mathematic and Natural Science Indraprasta University PGRI Jakarta Lecturer in Department of Landscape Architecture Bogor Agriculture University Lecturer in Study Program of Management Resort & Leisure Universitas Pendidikan Indonesia

The Resort II Salak Mountain has variety of landscape potential for created as ecotourism destination, especially the potential of the waterfall (curug) and sulphur crater (Kawah Ratu). The aim of this study was to identify and analyze the potential resources of the landscape to be created as ecotourism destination, Resort II Salak Mountain. This research was conducted through two phases: 1) identification of the attractions location that have potential resources for ecotourism destination, and 2) analysis of the level of potential resource of the landscape in each location using Analysis of Tourist Attraction Operational Destination (ATAOD). The study showed Resort II Salak Mountain has many ecotourism objects which have been used for ecotourism activities, such as hot spring baths, Curug Cigamea, Curug Ngumpet, Curug Seribu, Curug Pangeran, Curug Muara, Curug Cihurang, Kawah Ratu, camping ground, Curug Kondang and Curug Alami. The location of all waterfalls –curug, spread widely in the core zone for ecotourism. In the other hand, camping ground is located in the business zone, while Kawah Ratu is located in the natural forest, which is included in the buffer zone of Halimun-Salak National Park (HSNP). The result showed that the ecotourism objects with the highest potential value are Kawah Ratu, Curug Seribu, Curug Muara, Curug Kondang and Curug Ngumpet.

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Identification of Specific Characteristic of Kampung Jayengan as Community-based Industrial Tourism

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Procedia - Social and Behavioral Sciences 2016年 227卷 485-492页

作者： Winny Astuti Qomarun Alpha Febela Rufia A. Putri Dyah Widi Astuti Urban and Regional Planing Study Program Faculty of Engineering Universitas Sebelas Maret Jl. Ir. Sutami 36 A Kentingan Surakarta 57126 Indonesia Architecture Study Program Faculty of Engineering Universitas Muhammadiyah Surakarta Jalan Ahmad Yani Pabelan Surakarta Indonesia

The uniqueness of an area gives a lasting impression for special-interest tourists, which accelerate economic development. Therefore, the understanding local potencial become an embryo for the development of community-based tourism. Beside jewel craft, as the main potency, Kampung Jayengan also has strong potential in religion-based culinary and cultural traditions which are centered in Darussalam Mosque. In the future it could be a new tourism destination as part of the development of Surakarta as Creative Industrial-based City. This study aimed to identify the specific characteristics of the region as a basis for the development of community-based industrial tourism kampung.

关键词： special interest tourism kampung creative industry community-based Jewellery

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BABETTE MANGOLTE A Discontinuous Body

MILLENNIUM FILM JOURNAL

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MILLENNIUM FILM JOURNAL 2017年第66期 39-45页

作者： Sutcliffe, Alexandra Symons Whitney Independent Study Program New York NY 10013 USA Ctr Res Architecture New York NY 10013 USA

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Diversity and Utilization of Bamboo Plants in The Area of Hotel in Kedewatan Village, Ubud, Bali

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IOP Conference Series: Earth and Environmental Science 2017年第1期91卷

作者： N W F Utami N L M Pradnyawathi Landscape Architecture Study Program Faculty of Agriculture Udayana University Jl. P.B. Sudirman Denpasar Bali INDONESIA 80232 Agroecotechnology Study Program Faculty of Agriculture Udayana University Jl. P.B. Sudirman Denpasar Bali INDONESIA 80232

Bamboo or tiying (Balinese language) is a widely used non-timber plant in Indonesia especially in Bali. The presence of bamboo appertains to its ethno-botanical function of bamboo especially for rituals. However, there are other utilization of bamboo which is naturally grown or intentionally planted. Kedewatan as a famous place in northern Ubud, Bali have many lavish hotels with its natural environment and appealing place. The aims of this study is to invent bamboo species diversity and bamboo utilization on private areas of hotel in Kedewatan. Methods used in this study was field survey with observation and interview technic. Observation was implemented by purposive sampling methods by selecting hotel which adjacent to Ayung and Wos rivers. Interview was conducted with some key persons in charge on managing hotel garden. In addition, bamboo species identification was established through literature study. The results show that there are eleven bamboo species found on the survey area with most commonly employed species in the area were tiying tali (Gigantochloa apus (J.A. & J.H. Schultes) Kurz.) and tiying gading (Phyllostachys sulphurea (Carr.) A. e.t. C. Riv.) which were belong to exotic species. The areas which bamboo cultivated were welcome area as a hedgerow and near hotel lobby, between, outside and inside villa buildings, and naturally grown in the riverbanks with a good landscaping arrangement. Bamboo plantations were utilized to adorn and support the quality of the hotel building as well as to conserve soil and water along Ayung and Wos river canyons. The other utilization of bamboo was to facilitate ritual activity in Kedewatan village. They are allowed to ask for limited amount of bamboo culms with condition not to damage the physical appearance and function that desired by the hotel manager or hotel owner.

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Arbuscular mycorrhizal trees influence the latitudinal beta-diversity gradient of tree communities in forests worldwide

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NATURE COMMUNICATIONS 2021年第1期12卷 1-12页

作者： Zhong, Yonglin Chu, Chengjin Myers, Jonathan A. Gilbert, Gregory S. Lutz, James A. Stillhard, Jonas Zhu, Kai Thompson, Jill Baltzer, Jennifer L. He, Fangliang LaManna, Joseph A. Davies, Stuart J. Aderson-Teixeira, Kristina J. Burslem, David F. R. P. Alonso, Alfonso Chao, Kuo-Jung Wang, Xugao Gao, Lianming Orwig, David A. Yin, Xue Sui, Xinghua Su, Zhiyao Abiem, Iveren Bissiengou, Pulcherie Bourg, Norm Butt, Nathalie Cao, Min Chang-Yang, Chia-Hao Chao, Wei-Chun Chapman, Hazel Chen, Yu-Yun Coomes, David A. Cordell, Susan de Oliveira, Alexandre A. Du, Hu Fang, Suqin Giardina, Christian P. Hao, Zhanqing Hector, Andrew Hubbell, Stephen P. Janik, David Jansen, Patrick A. Jiang, Mingxi Jin, Guangze Kenfack, David Kral, Kamil Larson, Andrew J. Li, Buhang Li, Xiankun Li, Yide Lian, Juyu Lin, Luxiang Liu, Feng Liu, Yankun Liu, Yu Luan, Fuchen Luo, Yahuang Ma, Keping Malhi, Yadvinder McMahon, Sean M. McShea, William Memiaghe, Herve Mi, Xiangcheng Morecroft, Mike Novotny, Vojtech O'Brien, Michael J. den Ouden, Jan Parker, Geoffrey G. Qiao, Xiujuan Ren, Haibao Reynolds, Glen Samonil, Pavel Sang, Weiguo Shen, Guochun Shen, Zhiqiang Song, Guo-Zhang Michael Sun, I-Fang Tang, Hui Tian, Songyan Uowolo, Amanda L. Uriarte, Maria Wang, Bin Wang, Xihua Wang, Youshi Weiblen, George D. Wu, Zhihong Xi, Nianxun Xiang, Wusheng Xu, Han Xu, Kun Ye, Wanhui Yu, Mingjian Zeng, Fuping Zhang, Minhua Zhang, Yingming Zhu, Li Zimmerman, Jess K. Sun Yat Sen Univ Dept Ecol State Key Lab Biocontrol Guangzhou Peoples R China Sun Yat Sen Univ Sch Life Sci Guangzhou Peoples R China Washington Univ Dept Biol Campus Box 1137 St Louis MO 63130 USA Univ Calif Santa Cruz Dept Environm Studies Santa Cruz CA 95064 USA Utah State Univ Wildland Resources Dept Logan UT 84322 USA Swiss Fed Res Inst Forest Snow & Landscape Res WS Forest Resources & Management Birmensdorf Switzerland UK Ctr Ecol & Hydrol Bush Estate Penicuik Midlothian Scotland Wilfrid Laurier Univ Biol Dept Waterloo ON Canada Univ Alberta Dept Renewable Resources Edmonton AB Canada East China Normal Univ ECNU Alberta Joint Lab Biodivers Study Tiantong Natl Stn Forest Ecosyst Res Shanghai Peoples R China East China Normal Univ Sch Ecol & Environm Sci Zhejiang Tiantong Forest Ecosyst Natl Observat & Shanghai Peoples R China Marquette Univ Dept Biol Sci Milwaukee WI 53233 USA Smithsonian Trop Res Inst Forest Global Earth Observ Washington DC USA Natl Zool Pk Smithsonian Conservat Biol Inst Conservat Ecol Ctr Front Royal VA USA Univ Aberdeen Sch Biol Sci Aberdeen Scotland Natl Zool Pk Smithsonian Conservat Biol Inst Ctr Conservat & Sustainabil Washington DC USA Natl Chung Hsing Univ Int Master Program Agr Taichung Taiwan Chinese Acad Sci Inst Appl Ecol CAS Key Lab Forest Ecol & Management Beijing Peoples R China Chinese Acad Sci Kunming Inst Bot CAS Key Lab Plant Divers & Biogeog East Asia Beijing Peoples R China Harvard Univ Harvard Forest Petersham MA USA South China Agr Univ Coll Forestry & Landscape Architecture Guangzhou Peoples R China Univ Jos Dept Plant Sci & Technol Jos Nigeria Nigerian Montane Forest Project Ngel Nyaki Taraba State Nigeria Univ Canterbury Sch Biol Sci Christchurch New Zealand Ctr Natl Rech Sci & Technol Inst Rech Ecol Trop Libreville Gabon Univ Queensland Sch Biol Sci St Lucia Qld Australia Univ Queensland Ctr Biodivers & Conservat Sci St Lucia Qld Australia Chinese Acad Sci CAS Key Lab T

Arbuscular mycorrhizal (AM) and ectomycorrhizal (EcM) associations are critical for host-tree performance. However, how mycorrhizal associations correlate with the latitudinal tree beta-diversity remains untested. Using a global dataset of 45 forest plots representing 2,804,270 trees across 3840 species, we test how AM and EcM trees contribute to total beta-diversity and its components (turnover and nestedness) of all trees. We find AM rather than EcM trees predominantly contribute to decreasing total beta-diversity and turnover and increasing nestedness with increasing latitude, probably because wide distributions of EcM trees do not generate strong compositional differences among localities. Environmental variables, especially temperature and precipitation, are strongly correlated with beta-diversity patterns for both AM trees and all trees rather than EcM trees. Results support our hypotheses that latitudinal beta-diversity patterns and environmental effects on these patterns are highly dependent on mycorrhizal types. Our findings highlight the importance of AM-dominated forests for conserving global forest biodiversity. The relationship of mycorrhizal associations with latitudinal gradients in tree beta-diversity is unexplored. Using a global dataset approach, this study examines how trees with arbuscular mycorrhizal and ectomycorrhizal associations contribute to latitudinal beta-diversity patterns and the environmental controls of these patterns.

关键词： Biodiversity Biogeography

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Conservation of Underground Water with the Ecosystem Approach to the Development of the New Towns in Bogor, Tangerang, Bekasi (Botabek) Region

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Procedia - Social and Behavioral Sciences 2016年 227卷 720-727页

作者： Parino Rahardjo Djoko. M. Hartono Emirhadi Suganda Hadi Susilo Arifin Doctoral Student of Environmental Science Study Program University of Indonesia/Faculty of Urban & Regional Planning Department Faculty of Engineering University of Tarumanagara Jakarta Indonesia Civil Engineering Department Faculty of Engineering University of Indonesia Architecture Department Faculty of Engineering University of Indonesia Landscape Architecture Department Faculty of Agriculture. Bogor Agricultural University

The limited supply of clean water led to some residents in the city, as well as business and trade areas using underground water. Optimization of land used in the development of new towns and expanded impervious land surface, thus reducing infiltration capacity, resulting in an increased volume of runoff. The use of underground water and the reduced infiltration of rainwater resulted in a decrease in the underground water table. To maintain the underground water table and preventing land subsidence resulted from the use of underground water as raw material for clean water. The effort required is how doing underground water conservation. This paper discusses the development of new towns to assess the natural landscape as underground water conservation efforts on the development of the new town. The research method uses a quantitative approach to calculate the potential runoff using a soil conservation service, while to analyze the trend of changes in land cover using temporal spatial analysis, using descriptive analysis. The data used satellite imagery. The study found open green spaces, water bodies, and infrastructure in the form of green corridors can reduce runoff and maintain the underground water table.

关键词： Green open space impervious surface Landscape Ecology Runoff Urban Ecosystem

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