Article
Mathematical & Computational Biology
Brendan Behan, Francis Jeanson, Heena Cheema, Derek Eng, Fatema Khimji, Anthony L. Vaccarino, Tom Gee, Susan G. Evans, F. Chris MacPhee, Fan Dong, Shahab Shahnazari, Alana Sparks, Emily Martens, Bianca Lasalandra, Stephen R. Arnott, Stephen C. Strother, Mojib Javadi, Moyez Dharsee, Kenneth R. Evans, Kirk Nylen, Tom Mikkelsen
Summary: The sharing of health research data can greatly impact disease understanding and patient outcomes within the healthcare ecosystem. However, to achieve this potential, data must meet the FAIR principles of findability, accessibility, interoperability, and reusability. The Ontario Brain Institute has pioneered data sharing activities aligned with FAIR principles in neuroscience through its Brain-CODE platform and services.
FRONTIERS IN NEUROINFORMATICS
(2023)
Article
Oncology
Andrey Fedorov, William J. R. Longabaugh, David Pot, David A. Clunie, Steve Pieper, Hugo J. W. L. Aerts, Andre Homeyer, Rob Lewis, Afshin Akbarzadeh, Dennis Bontempi, William Clifford, Markus D. Herrmann, Henning Hoefener, Igor Octaviano, Chad Osborne, Suzanne Paquette, James Petts, Davide Punzo, Madelyn Reyes, Daniela P. Schacherer, Mi Tian, George White, Erik Ziegler, Ilya Shmulevich, Todd Pihl, Ulrike Wagner, Keyvan Farahani, Ron Kikinis
Summary: The NCI's CRDC aims to establish a national cloud-based data science infrastructure, with IDC as a new component dedicated to supporting cancer imaging research. IDC enables a broad spectrum of cancer researchers to easily access and explore the value of deidentified imaging data and support integrated analyses with nonimaging data.
Review
Computer Science, Information Systems
Neha Thakur, Avtar Singh, A. L. Sangal
Summary: This paper presents a systematic review of existing cloud service selection approaches, analyzing them across eight dimensions such as decision-making methods, context, and cloud service performance parameters. The study identifies open research issues and critical challenges in cloud service selection. The contribution of this research lies in focusing on state-of-the-art approaches, highlighting their benefits and drawbacks, offering a taxonomy, and identifying future research directions.
COMPUTER SCIENCE REVIEW
(2022)
Article
Biotechnology & Applied Microbiology
Ling Cai, Chengyue Xing, Yi Deng
Summary: This research focuses on the application of digital urban management integration, designing a subsystem to address urban management issues and utilizing cloud computing as a solid foundation for digital cities. Practice shows that digital cities can effectively improve urban management, with the aim of exploring construction based on cloud computing data centers.
ENVIRONMENTAL TECHNOLOGY & INNOVATION
(2021)
Article
Neurosciences
Jordi Huguet, Carles Falcon, David Fuste, Sergi Girona, David Vicente, Jose Luis Molinuevo, Juan Domingo Gispert, Gregory Operto
Summary: The paper proposes a practical model guided by core principles to address the challenge of dealing with large imaging datasets. This model is based on the experience from a long-term research center and provides a toolkit ecosystem to help improve quality control and facilitate data sharing.
FRONTIERS IN NEUROSCIENCE
(2021)
Article
Computer Science, Interdisciplinary Applications
Daniela P. Schacherer, Markus D. Herrmann, David A. Clunie, Henning Hoefener, William Clifford, William J. R. Longabaugh, Steve Pieper, Ron Kikinis, Andrey Fedorov, Andre Homeyer
Summary: This study explores the potential of the NCI Imaging Data Commons (IDC) in facilitating reproducibility in computational pathology research. The results of the experiments show that the IDC can achieve a high level of experiment reproducibility, but there are practical limits.
COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE
(2023)
Article
Computer Science, Interdisciplinary Applications
Nicolas Roehri, Samuel Medina Villalon, Aude Jegou, Bruno Colombet, Bernard Giusiano, Aurelie Ponz, Fabrice Bartolomei, Christian-George Benar
Summary: Multicentre studies are crucial for confirming hypotheses, but are often hindered by the lack of established standards and data management complexity. The Brain Imaging Data Structure (BIDS) initiative aims to organize and describe neuroimaging data, with two software programs, BIDS Manager and BIDS Uploader, developed to facilitate the implementation of multicentre studies by providing a standardized framework.
Article
Multidisciplinary Sciences
Harry Carey, Michael Pegios, Lewis Martin, Chris Saleeba, Anita J. Turner, Nicholas A. Everett, Ingvild E. Bjerke, Maja A. Puchades, Jan G. Bjaalie, Simon Mcmullan
Summary: Registration of data to a common frame of reference is crucial in analyzing and integrating diverse neuroscientific data. The traditional methods for registration are time-consuming and rely on expertise. However, using the neural network DeepSlice, we were able to significantly improve the speed while maintaining the accuracy of registering mouse brain histological images to the Allen Brain Common Coordinate Framework.
NATURE COMMUNICATIONS
(2023)
Article
Biology
Alejandro de la Vega, Roberta Rocca, Ross W. Blair, Christopher J. Markiewicz, Jeff Mentch, James D. Kent, Peer Herholz, Satrajit S. Ghosh, Russell A. Poldrack, Tal Yarkoni
Summary: Neuroscout is an end-to-end platform for analyzing naturalistic fMRI data, which automatically annotates stimuli from multiple ecologically-valid datasets and reduces the burden of reproducible research. Through validating the automatic feature extraction approach, it has the potential to support more robust fMRI research and democratize fMRI research.
Article
Computer Science, Information Systems
Qinlu He, Fan Zhang, Genqing Bian, Weiqi Zhang, Dongli Duan, Zhen Li, Chen Chen
Summary: This paper investigates a data routing strategy based on distributed Bloom Filter. By using superchunks as the basic unit of data routing, the system throughput is improved. The feasibility of the strategy is validated through experiments, and its advantages over other routing strategies are demonstrated.
Review
Neurosciences
Sook-Lei Liew, Artemis Zavaliangos-Petropulu, Neda Jahanshad, Catherine E. Lang, Kathryn S. Hayward, Keith R. Lohse, Julia M. Juliano, Francesca Assogna, Lee A. Baugh, Anup K. Bhattacharya, Bavrina Bigjahan, Michael R. Borich, Lara A. Boyd, Amy Brodtmann, Cathrin M. Buetefisch, Winston D. Byblow, Jessica M. Cassidy, Adriana B. Conforto, R. Cameron Craddock, Michael A. Dimyan, Adrienne N. Dula, Elsa Ermer, Mark R. Etherton, Kelene A. Fercho, Chris M. Gregory, Shahram Hadidchi, Jess A. Holguin, Darryl H. Hwang, Simon Jung, Steven A. Kautz, Mohamed Salah Khlif, Nima Khoshab, Bokkyu Kim, Hosung Kim, Amy Kuceyeski, Martin Lotze, Bradley J. MacIntosh, John L. Margetis, Feroze B. Mohamed, Fabrizio Piras, Ander Ramos-Murguialday, Genevieve Richard, Pamela Roberts, Andrew D. Robertson, Jane M. Rondina, Natalia S. Rost, Nerses Sanossian, Nicolas Schweighofer, Na Jin Seo, Mark S. Shiroishi, Surjo R. Soekadar, Gianfranco Spalletta, Cathy M. Stinear, Anisha Suri, Wai Kwong W. Tang, Gregory T. Thielman, Daniela Vecchio, Arno Villringer, Nick S. Ward, Emilio Werden, Lars T. Westlye, Carolee Winstein, George F. Wittenberg, Kristin A. Wong, Chunshui Yu, Steven C. Cramer, Paul M. Thompson
Summary: The ENIGMA Stroke Recovery working group aims to understand the relationship between brain and behavior using meta- and mega-analytic approaches. They have developed neuroinformatics protocols and methods to manage large-scale data from over 2,100 stroke patients. The challenges and recommendations for data harmonization in stroke research are discussed.
HUMAN BRAIN MAPPING
(2022)
Article
Computer Science, Artificial Intelligence
Yuxiao Du, Yuxing Li, Zhuocheng Wu, Feng Chen, Zhiheng Chen, Yinglin Li
Summary: In this study, a depth camera was used for noncontact measurement of the human body. Through coordinate transformation and point cloud data preprocessing, the complete outline of the human body was obtained, and the measurement results were within the range of relevant standard accuracy.
INTERNATIONAL JOURNAL OF INTELLIGENT SYSTEMS
(2022)
Article
Computer Science, Information Systems
Lemuel R. Waitman, Xing Song, Dammika Lakmal Walpitage, Daniel C. Connolly, Lav P. Patel, Mei Liu, Mary C. Schroeder, Jeffrey J. VanWormer, Abu Saleh Mosa, Ernest T. Anye, Ann M. Davis
Summary: The study introduces a reusable environment called GROUSE that integrates hospital and EHR data with state-wide Medicare and Medicaid claims to identify obesity and related comorbidities. Results show that diagnosis codes from EHR and claims sources underreport obesity compared to BMI measures, but common comorbidities are more often available from claims diagnoses codes.
JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION
(2022)
Article
Mathematical & Computational Biology
Tinashe M. Tapera, Matthew Cieslak, Max Bertolero, Azeez Adebimpe, Geoffrey K. Aguirre, Ellyn R. Butler, Philip A. Cook, Diego Davila, Mark A. Elliott, Sophia Linguiti, Kristin Murtha, William Tackett, John A. Detre, Theodore D. Satterthwaite
Summary: The recent focus on reproducibility in neuroimaging studies has led academic centers to use cloud-based imaging databases like Flywheel. To address the challenges of curating BIDS data on Flywheel, FlywheelTools software toolbox was developed to accelerate reproducible neuroscience research on the platform.
FRONTIERS IN NEUROINFORMATICS
(2021)
Article
Computer Science, Information Systems
Xinying Wang, Cong Xu, Ke Wang, Feng Yan, Dongfang Zhao
Summary: This article investigates the selection of memory scaling mechanisms for deploying applications on big data systems in public clouds. By analyzing the trade-off between performance and cost of physical memory and virtual memory, and proposing a just-in-time migration method, this study demonstrates that these techniques can improve performance and reduce costs.
IEEE TRANSACTIONS ON BIG DATA
(2022)
Article
Forestry
Chikage Todo, Chie Tokoro, Keitaro Yamase, Toko Tanikawa, Mizue Ohashi, Hidetoshi Ikeno, Masako Dannoura, Kouhei Miyatani, Ryuusei Doi, Yasuhiro Hirano
FOREST ECOLOGY AND MANAGEMENT
(2019)
Article
Biochemistry & Molecular Biology
Masahiko Morita, Kazuro Shimokawa, Masaomi Nishimura, Sakiko Nakamura, Yuki Tsujimura, Satoko Takemoto, Takehiro Tawara, Hideo Yokota, Shuhei Wemler, Daisuke Miyamoto, Hidetoshi Ikeno, Akira Sato, Teiichi Furuichi, Norio Kobayashi, Yoshihiro Okumura, Yoko Yamaguchi, Yuko Okamura-Oho
NUCLEIC ACIDS RESEARCH
(2019)
Review
Entomology
Hiroyuki Ai, Ryuichi Okada, Midori Sakura, Thomas Wachtler, Hidetoshi Ikeno
Article
Geosciences, Multidisciplinary
Keitaro Yamase, Toko Tanikawa, Masako Dannoura, Chikage Todo, Tomonori Yamamoto, Hidetoshi Ikeno, Mizue Ohashi, Kenji Aono, Ryuusei Doi, Yasuhiro Hirano
Article
Cell Biology
Shu Kondo, Takahiro Takahashi, Nobuhiro Yamagata, Yasuhito Imanishi, Hidetaka Katow, Shun Hiramatsu, Katrina Lynn, Ayako Abe, Ajayrama Kumaraswamy, Hiromu Tanimoto
Article
Entomology
Duy Long Pham, Yasuto Ito, Ryuichi Okada, Hidetoshi Ikeno, Haruna Kazama, Naoki Mori, Michimasa Yamasaki
ENTOMOLOGIA EXPERIMENTALIS ET APPLICATA
(2020)
Article
Forestry
Toko Tanikawa, Hidetoshi Ikeno, Chikage Todo, Keitaro Yamase, Mizue Ohashi, Toru Okamoto, Takeo Mizoguchi, Katsuhiro Nakao, Shinji Kaneko, Atsushi Torii, Yoshiyuki Inagaki, Asami Nakanishi, Yasuhiro Hirano
Summary: The soil held by tree roots is significantly heavier than the tree biomass, helping to balance the weight above and belowground. Actual measurements of root-soil plate mass show that soil plays a crucial role in overall tree mass. Aboveground allometric indices are useful for estimating belowground mass to understand tree anchorage.
TREES-STRUCTURE AND FUNCTION
(2021)
Article
Entomology
Tetsu Yamamoto, Michio Sugahara, Ryuichi Okada, Hidetoshi Ikeno
Summary: The study revealed that the piping signals of two honeybee species, Apis cerana and Apis mellifera, had different temporal structures. The tooting of A. cerana consisted of almost one long syllable, while that of A. mellifera was constructed from several syllables. The quacking of both species comprised around 50 short syllables, but the duration and period of the syllables of A. cerana were about half those of A. mellifera.
Article
Computer Science, Interdisciplinary Applications
Mathew Birdsall Abrams, Jan G. Bjaalie, Samir Das, Gary F. Egan, Satrajit S. Ghosh, Wojtek J. Goscinski, Jeffrey S. Grethe, Jeanette Hellgren Kotaleski, Eric Tatt Wei Ho, David N. Kennedy, Linda J. Lanyon, Trygve B. Leergaard, Helen S. Mayberg, Luciano Milanesi, Roman Moucek, J. B. Poline, Prasun K. Roy, Stephen C. Strother, Tong Boon Tang, Paul Tiesinga, Thomas Wachtler, Daniel K. Wojcik, Maryann E. Martone
Summary: There is a great need for coordination around standards and best practices in neuroscience to address challenges in data science. Developing community standards and gaining their adoption is difficult, as the current landscape is characterized by a lack of robust, validated standards and a plethora of underdeveloped and underutilized standards and best practices. An independent organization, the International Neuroinformatics Coordinating Facility (INCF), is dedicated to promoting data sharing in neuroscience and has implemented procedures for evaluating and endorsing community standards and best practices.
Article
Computer Science, Cybernetics
Michael Schmuker, Ruediger Kupper, Ad Aertsen, Thomas Wachtler, Marc-Oliver Gewaltig
Summary: A mechanism is proposed to detect feature homogeneity in visual areas based on latency coding and spike time coincidence, potentially supporting rapid image segmentation. Further analysis shows how neuronal crosstalk affects the mechanism's performance. The detrimental effects of crosstalk can be mitigated through delayed feed-forward inhibition that shapes bi-phasic post-synaptic events.
BIOLOGICAL CYBERNETICS
(2021)
Correction
Computer Science, Interdisciplinary Applications
Mathew Birdsall Abrams, Jan G. Bjaalie, Samir Das, Gary F. Egan, Satrajit S. Ghosh, Wojtek J. Goscinski, Jeffrey S. Grethe, Jeanette Hellgren Kotaleski, Eric Tatt Wei Ho, David N. Kennedy, Linda J. Lanyon, Trygve B. Leergaard, Helen S. Mayberg, Luciano Milanesi, Roman Moucek, J. B. Poline, Prasun K. Roy, Stephen C. Strother, Tong Boon Tang, Paul Tiesinga, Thomas Wachtler, Daniel K. Wojcik, Maryann E. Martone
Article
Forestry
Chikage Todo, Hidetoshi Ikeno, Keitaro Yamase, Toko Tanikawa, Mizue Ohashi, Masako Dannoura, Toshifumi Kimura, Yasuhiro Hirano
Summary: This study proposed a new method to easily obtain root point data from 3D laser scanner's point cloud data for reconstructing root system architecture. The accuracy of data obtained from 3D laser scanner measurement was found to be similar to intensive manual measurements. The reconstructed root system architecture was simpler but still accurately represented the main coarse root segments.
Article
Ornithology
Brigitte Berger-Geiger, Georg Heine, Ajayrama Kumaraswamy, C. Giovanni Galizia
Summary: The study shows that Montagu's Harriers exhibit different behaviors before and after breeding. Males and the majority of females return to their old nest site upon arrival from spring migration, spending days to weeks on mate choice and site inspection. Female movements decrease during incubation and early nesting, but increase significantly during late nesting and post-fledging periods. Non-breeding females exhibit more activity in defending nests against predators in the colony. Females with successful broods initiate migration earlier and spend less time in Spain than non-breeders or those with predated nests.
JOURNAL OF ORNITHOLOGY
(2022)
Article
Multidisciplinary Sciences
Malin Sandstrom, Mathew Abrams, Jan G. Bjaalie, Mona Hicks, David N. Kennedy, Arvind Kumar, Jean-Baptiste Poline, Prasun K. Roy, Paul Tiesinga, Thomas Wachtler, Wojtek J. Goscinski
Summary: Repositories and science gateways are vital resources for the neuroscience community, but users struggle to find the most suitable services. INCF has developed recommendations and criteria for selecting, establishing, and running repositories or scientific gateways with a FAIR perspective.
Article
Multidisciplinary Sciences
Yannan Su, Thomas Wachtler, Zhuanghua Shi
Summary: The perception of a visual stimulus can be influenced by its surrounding context, such as reference repulsion. However, it is unclear at which stage of visual processing this phenomenon occurs. This study found that a reference can influence late visual processing, and the explicit discrimination choices between reference and stimulus can also affect the magnitude of the repulsion effect.
SCIENTIFIC REPORTS
(2023)