Article
Computer Science, Interdisciplinary Applications
Cyrille Ahmed Midingoyi, Christophe Pradal, Andreas Enders, Davide Fumagalli, Helene Raynal, Marcello Donatelli, Ioannis N. Athanasiadis, Cheryl Porter, Gerrit Hoogenboom, Dean Holzworth, Frederick Garcia, Peter Thorburn, Pierre Martre
Summary: Process-based crop models are widely used tools for analyzing and simulating agricultural systems' responses to various factors. The lack of efficient methods for exchanging biophysical processes between modeling platforms makes intercomparison and improvement of crop simulation models challenging. Crop2ML is a modeling framework that allows the description and assembly of crop model components independently of the formalism of modeling platforms, facilitating the exchange of components between platforms.
ENVIRONMENTAL MODELLING & SOFTWARE
(2021)
Article
Computer Science, Hardware & Architecture
David Biancolin, Albert Magyar, Sagar Karandikar, Alon Amid, Borivoje Nikolic, Jonathan Bachrach, Krste Asanovic
Summary: The open-source hardware community offers a variety of processors and accelerators, but effectively combining them into a complete SoC remains a challenge. Researchers have proposed a design flow for evaluating the seamless integration of accelerators into a complete SoC through rapid FPGA prototyping.
Article
Agronomy
Francisco Puig, Juan Antonio Rodriguez Diaz, Maria Auxiliadora Soriano
Summary: Smart irrigation is becoming increasingly important in agriculture, but implementing it can be challenging for farmers. We have developed a low-cost, open-source IoT system for smart irrigation that can be integrated with other platforms and supports a wide range of sensors. The system has been tested on an olive farm, and the results show the advantages of using these technologies over traditional methods.
Article
Education & Educational Research
David John Lemay, Ram B. Basnet, Tenzin Doleck
Summary: The study examined users' intentions to switch to Linux-based open-source operating systems, finding that perceived need and behavioral intention have the strongest influence, followed by social norms and uncertainty costs affecting inertia. Incumbent system habit and perceived switching cost had smaller effects on inertia.
EDUCATION AND INFORMATION TECHNOLOGIES
(2022)
Article
Agronomy
Minguo Liu, Mei Yang, Huimin Yang
Summary: This article presents an open-source software package called simET, which aims to accurately estimate crop evapotranspiration (ETc) and soil water balance. The package includes various functions and models for different crops.
Article
Agronomy
Abdur Rahim Safi, Poolad Karimi, Marloes Mul, Abebe Chukalla, Charlotte de Fraiture
Summary: This paper introduces a standard approach using open-source remote sensing data to diagnose reasons behind crop water productivity (WP) variations, and demonstrates the feasibility and practical usefulness of the diagnostic framework through a case study.
AGRICULTURAL WATER MANAGEMENT
(2022)
Article
Environmental Sciences
Yanling Li, Weiping Chen, Yang Yang, Tianqi Wang, Yating Dai
Summary: A source-specific risk assessment model was developed to estimate the intake risk of cadmium from wheat, with wastewater and industrial residues mixed source being the dominant contamination sources. Regionalized risk management strategies were proposed based on the assessment results to minimize Cd input and health risks.
ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY
(2021)
Article
Computer Science, Interdisciplinary Applications
Cyrille Ahmed Midingoyi, Christophe Pradal, Andreas Enders, Davide Fumagalli, Patrice Lecharpentier, Helene Raynal, Marcello Donatelli, Davide Fanchini, Ioannis N. Athanasiadis, Cheryl Porter, Gerrit Hoogenboom, F. A. A. Oliveira, Dean Holzworth, Pierre Martre
Summary: This study presents a reverse engineering approach to automatically extract and transform meta-information and algorithms of existing crop biophysical models into a platform-independent model component. The system demonstrates good extensibility across different platforms using the Crop2ML concepts and transformation system.
ENVIRONMENTAL MODELLING & SOFTWARE
(2023)
Article
Energy & Fuels
Pawel Dymora, Miroslaw Mazurek, Bartosz Sudek
Summary: With the increasing number of users, the importance of traffic balancing in web services has become crucial, as evidenced by a comparative analysis of open-source solutions for performance. Test results show that optimizing network traffic balancing distribution is essential for energy-efficient data centers.
Article
Biotechnology & Applied Microbiology
Chenxiao Xue, Caixia Cao
Summary: By using CRISPR-Cas base editing and prime editing, we manipulated upstream open reading frames - eukaryotic translational control elements - in rice to regulate translation levels. This enabled predictable and desired downregulation of gene expression, leading to quantitative phenotypic changes and crop improvement.
NATURE BIOTECHNOLOGY
(2023)
Article
Multidisciplinary Sciences
Joseph Aylett-Bullock, Carolina Cuesta-Lazaro, Arnau Quera-Bofarull, Miguel Icaza-Lizaola, Aidan Sedgewick, Henry Truong, Aoife Curran, Edward Elliott, Tristan Caulfield, Kevin Fong, Ian Vernon, Julian Williams, Richard Bower, Frank Krauss
Summary: June is an open-source framework for detailed simulation of epidemics based on social interactions in a virtual population, with flexible parameterization. The paper applies June to model the spread of COVID-19 in England, discussing the quality of initial model outputs.
ROYAL SOCIETY OPEN SCIENCE
(2021)
Article
Multidisciplinary Sciences
Yunlin Li, Fengye Wu, Qinyan Wu, Wenya Liu, Guanghui Li, Benxing Yao, Ran Xiao, Yudie Hu, Junsong Wang
Summary: This study presents a low-cost and automatic zebrafish behavior assay apparatus for evaluating the neurobehavioral performance of zebrafish. It utilizes a custom-written behavior analysis algorithm, data processing on a Raspberry Pi, and implements Kalman filter algorithm and ROI region to increase accuracy. The setup was also used to analyze zebrafish behavioral changes under different alcohol concentrations, demonstrating its reliability and accuracy.
Article
Oncology
Christian Ronn Hansen, Gareth Price, Matthew Field, Nis Sarup, Ruta Zukauskaite, Jorgen Johansen, Jesper Grau Eriksen, Farhannah Aly, Andrew McPartlin, Lois Holloway, David Thwaites, Carsten Brink
Summary: This study demonstrates the use of federated learning in performing stratified Cox regression survival analysis on larynx cancer patients from multiple countries, avoiding the risk of data leakage. The results show that tumor volume and performance status are the main factors influencing survival.
RADIOTHERAPY AND ONCOLOGY
(2022)
Article
Oncology
Christian Ronn Hansen, Gareth Price, Matthew Field, Nis Sarup, Ruta Zukauskaite, Jorgen Johansen, Jesper Grau Eriksen, Farhannah Aly, Andrew McPartlin, Lois Holloway, David Thwaites, Carsten Brink
Summary: This study developed open-source distributed learning software based on a stratified Cox proportional hazard model, and validated the Egelmeer et al. MAASTRO survival model across two hospitals in two countries. The software successfully validated and suggested a minor update to the original survival model without central access to patient sensitive information.
RADIOTHERAPY AND ONCOLOGY
(2022)
Article
Chemistry, Analytical
Sergio Paniego, Vinay Sharma, Jose Maria Canas
Summary: This paper introduces an open-source software called Detection Metrics for assessing the performance of deep learning neural network models in visual object detection. It provides objective performance metrics and supports various datasets and deep learning frameworks, enabling fair comparison among different models. The software also offers tools for dataset and model management, visualization, and conversion. It has been experimentally validated and used in research projects for model selection and comparison. The importance of this software is that it facilitates the development of deep learning applications and research in the field of object detection.
Article
Agriculture, Multidisciplinary
R. Mompremier, Y. Her, G. Hoogenboom, J. Song
Summary: The lack of environmental management and conservation practices in Haitian watersheds leads to impaired natural resources and agricultural productivity. Deforestation to compensate for reduced crop production worsens the situation. The study demonstrates that afforestation can improve water availability and stability, increasing agricultural production.
AGRICULTURE ECOSYSTEMS & ENVIRONMENT
(2022)
Article
Environmental Sciences
Mubashra Yasin, Ashfaq Ahmad, Tasneem Khaliq, Muhammad Habib-ur-Rahman, Salma Niaz, Thomas Gaiser, Iqra Ghafoor, Hafiz Suboor ul Hassan, Muhammad Qasim, Gerrit Hoogenboom
Summary: Future climate change poses significant threats to sustainable maize production in arid and semi-arid regions, but these impacts can be minimized through the adoption of modern agricultural tools. Research indicates that rising temperatures in the future may lead to reduced maize yields, but adjusting planting dates and utilizing heat and drought-resistant hybrids could help mitigate these effects.
ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH
(2022)
Article
Agriculture, Multidisciplinary
Alireza Araghi, Christopher J. Martinez, Jorgen E. Olesen, Gerrit Hoogenboom
Summary: This study aimed to identify the most appropriate gridded temperature data (GTD) for crop simulation modeling. Results showed that AgCFSR, AgMERRA, PGF, and AgERA5 had the best performance, while NCEP and GLDAS had the weakest performance. AgERA5 can be recommended for temperature-related agricultural simulations for the study area in Iran and similar environmental regions.
COMPUTERS AND ELECTRONICS IN AGRICULTURE
(2022)
Article
Plant Sciences
Sibylle Dueri, Hamish Brown, Senthold Asseng, Frank Ewert, Heidi Webber, Mike George, Rob Craigie, Jose Rafael Guarin, Diego N. L. Pequeno, Tommaso Stella, Mukhtar Ahmed, Phillip D. Alderman, Bruno Basso, Andres G. Berger, Gennady Bracho Mujica, Davide Cammarano, Yi Chen, Benjamin Dumont, Ehsan Eyshi Rezaei, Elias Fereres, Roberto Ferrise, Thomas Gaiser, Yujing Gao, Margarita Garcia-Vila, Sebastian Gayler, Zvi Hochman, Gerrit Hoogenboom, Kurt C. Kersebaum, Claas Nendel, Jorgen E. Olesen, Gloria Padovan, Taru Palosuo, Eckart Priesack, Johannes W. M. Pullens, Alfredo Rodriguez, Reimund P. Roetter, Margarita Ruiz Ramos, Mikhail A. Semenov, Nimai Senapati, Stefan Siebert, Amit Kumar Srivastava, Claudio Stockle, Iwan Supit, Fulu Tao, Peter Thorburn, Enli Wang, Tobias Karl David Weber, Liujun Xiao, Chuang Zhao, Jin Zhao, Zhigan Zhao, Yan Zhu, Pierre Martre
Summary: Crop multi-model ensembles (MME) have been proven effective in improving simulation accuracy in modelling experiments, but their ability to capture crop responses to changes in sowing dates and densities needs further investigation. This study used a MME of 29 wheat crop models to predict the effects of changing sowing dates and rates on yield and yield components in New Zealand. The results showed that the MME performed well under standard sowing conditions, but failed to simulate early sowing and high sowing rates accurately. Improvements are needed in the models to account for tiller competition and early tiller senescence under these conditions.
JOURNAL OF EXPERIMENTAL BOTANY
(2022)
Article
Energy & Fuels
Xiuzhi Chen, Chang Liu, Pieter van Oel, Mesfin Mergia Mekonnen, Kelly R. Thorp, Tuo Yin, Jinyan Wang, Tahir Muhammad, Yunkai Li
Summary: This study selected China as a case to assess the water footprint and carbon footprint of hydropower for the first time in spatial and temporal dimensions. The results showed that the total water and carbon footprints of hydropower in China are significant and exceed sustainable development goals in some aspects. This indicates the need for greater emphasis on environmental protection and sustainability in hydropower development.
Article
Agronomy
Bruce A. Kimball, Kelly R. Thorp, Kenneth J. Boote, Claudio Stockle, Andrew E. Suyker, Steven R. Evett, David K. Brauer, Gwen G. Coyle, Karen S. Copeland, Gary W. Marek, Paul D. Colaizzi, Marco Acutis, Seyyedmajid Alimagham, Sotirios Archontoulis, Faye Babacar, Zoltan Barcza, Bruno Basso, Patrick Bertuzzi, Julie Constantin, Massimiliano De Antoni Migliorati, Benjamin Dumont, Jean-Louis Durand, Nandor Fodor, Thomas Gaiser, Pasquale Garofalo, Sebastian Gayler, Luisa Giglio, Robert Grant, Kaiyu Guan, Gerrit Hoogenboom, Qianjing Jiang, Soo-Hyung Kim, Isaya Kisekka, Jon Lizaso, Sara Masia, Huimin Meng, Valentina Mereu, Ahmed Mukhtar, Alessia Perego, Bin Peng, Eckart Priesack, Zhiming Qi, Vakhtang Shelia, Richard Snyder, Afshin Soltani, Donatella Spano, Amit Srivastava, Aimee Thomson, Dennis Timlin, Antonio Trabucco, Heidi Webber, Tobias Weber, Magali Willaume, Karina Williams, Michael van der Laan, Domenico Ventrella, Michelle Viswanathan, Xu Xu, Wang Zhou
Summary: Accurate simulation of crop water use is important for assessing the impact of climate change on crop productivity and aiding irrigation scheduling. This study compared 41 maize growth models and found that several models were able to simulate crop water use effectively. However, there were variations in simulation accuracy across different sites, seasons, and irrigation levels. Factors that need improvement include handling of humidity and wind, as well as simulation methods for soil water evaporation. Nonetheless, older models that have been widely tested and used performed well in simulating crop water use, indicating the importance of model testing and improvement.
AGRICULTURAL AND FOREST METEOROLOGY
(2023)
Article
Agronomy
Diaa Eldin M. Elshikha, Guangyao Wang, Peter M. Waller, Douglas J. Hunsaker, David Dierig, Kelly R. Thorp, Alison Thompson, Matthew E. Katterman, Matthew T. Herritt, Eduardo Bautista, Dennis T. Ray, Gerard W. Wall
Summary: In this study, different deficit irrigation strategies were tested on guayule plants in central Arizona. The results showed that irrigating every other time can significantly increase water productivity of guayule without reducing yield.
AGRICULTURAL WATER MANAGEMENT
(2023)
Article
Environmental Sciences
Robert W. Malone, Anna Radke, Steph Herbstritt, Huaiqing Wu, Zhiming Qi, Bryan D. Emmett, Matthew J. Helmers, Lisa A. Schulte, Gary W. Feyereisen, Peter L. O'Brien, John L. Kovar, Natalia Rogovska, Eileen J. Kladivko, Kelly R. Thorp, Tom C. Kaspar, Dan B. Jaynes, Douglas L. Karlen, Tom L. Richard
Summary: Large-scale adoption of winter rye as a cover crop can reduce nitrogen loss, carbon emissions, and provide renewable natural gas and carbon storage benefits. Based on simulations in the North Central US, harvesting fertilized winter rye before soybean planting can reduce nitrogen loads to the Gulf of Mexico by 27%, and provide 18 million Mg yr(-1) of biomass, equivalent to 0.21 EJ yr(-1) of biogas energy content or 3.5 times the 2022 US cellulosic biofuel production. Capturing CO2 from rye digestion and sequestering it in underground reservoirs could mitigate 7.5 million Mg CO2 yr(-1). Hotspots were identified where 400 Gg yr(-1) of rye could be sourced within a 121 km radius, contributing to nitrogen loss reduction and biomass production.
ENVIRONMENTAL RESEARCH LETTERS
(2023)
Article
Multidisciplinary Sciences
Xiuzhi Chen, Yue Hou, Thomas Kastner, Liu Liu, Yuqian Zhang, Tuo Yin, Mo Li, Arunima Malik, Mengyu Li, Kelly R. Thorp, Siqi Han, Yaoze Liu, Tahir Muhammad, Jianguo Liu, Yunkai Li
Summary: This study identifies and quantifies the flows of physical and virtual nutrients within the global agricultural trade network. The study shows that these flows have varying effects on natural resources in different countries. The findings suggest that reducing inefficient trade flows can enhance resource conservation and environmental sustainability. These results are important for understanding the global nutrient dynamics and improving nutrient use efficiency in a hyper-globalized world.
NATURE COMMUNICATIONS
(2023)
Review
Environmental Sciences
Ibukun T. T. Ayankojo, Kelly R. R. Thorp, Alison L. L. Thompson
Summary: High-throughput plant phenotyping (HTPP) is the application of modern information technologies to evaluate the effects of genetics, environment, and management on plant traits expression in breeding programs. This review identifies the advantages and limitations of terrestrial and sUAS platforms, summarizes imaging techniques and image processing methods used, describes quantified plant traits, and compares estimation accuracy across traits, platforms, crops, and sensors. The review concludes that sUAS technology is a practical and cost-effective solution for rapid HTPP, especially for plant growth traits, and that sensor performance for crop trait estimation varies depending on the platform and trait of interest.
Article
Environmental Sciences
Hadiqa Maqsood, Douglas J. J. Hunsaker, Peter Waller, Kelly R. R. Thorp, Andrew French, Diaa Eldin Elshikha, Reid Loeffler
Summary: The WINDS model was developed to support irrigated-crop management in the U.S. Southwest by simulating soil water balance and evapotranspiration dynamics. The model demonstrated its accuracy through calibration and comparison with field measurements. It also successfully reproduced measured crop evapotranspiration during the growing season. This paper introduces the online WINDS model.
Article
Computer Science, Software Engineering
Josh Brekel, Kelly R. Thorp, Kendall C. DeJonge, Thomas J. Trout
Summary: The pyfao56 software package is a Python-based implementation of the FAO-56 standardized evapotranspiration (ET) methodologies. This update improves pyfao56 by fixing a major bug, expanding reference ET calculation options, adding functionality for specifying variable soil characteristics, including optional water balance enhancements, and enabling the use of constant or variable depletion fraction (p). The updates increase software versatility while maintaining core functionality.
Article
Multidisciplinary Sciences
Mohammad Kamruzzaman, Shahriar Wahid, Shamsuddin Shahid, Edris Alam, Mohammed Mainuddin, H. M. Touhidul Islam, Jeapil Cho, Md Mizanur Rahman, Jatish Chandra Biswas, Kelly R. Thorp
Summary: Understanding changes in precipitation and temperature is crucial for assessing environmental risks and planning adaptation measures. This study used 18 Global Climate Models (GCMs) to project precipitation and temperature in Bangladesh and found significant increases in both variables in the future. The projected changes could lead to increased flooding, landslides, and negative impacts on various sectors, highlighting the need for localized adaptation strategies.
Article
Agricultural Engineering
Gary W. Marek, Steve R. Evett, Kelly R. Thorp, Kendall C. DeJonge, Thomas H. Marek, David K. Brauer
Summary: Effective irrigation systems are crucial for saving groundwater resources. Center-pivot sprinkler systems are widely used in the U.S. Southern High Plains, but their evaporative losses need to be quantified. This study compared evapotranspiration values for different irrigation methods and found that evaporative losses extended beyond the day of irrigation.
JOURNAL OF THE ASABE
(2023)
Article
Agronomy
Hossein Babazadeh, Mandi Sarai Tabriz, Gerrit Hoogenboom
Summary: This research aims to optimize water productivity and crop production simultaneously under deficit irrigation management conditions using genetic algorithm and simulated annealing algorithm. The results show that genetic algorithm performs better in simultaneous optimization of the two objective functions.
ROMANIAN AGRICULTURAL RESEARCH
(2022)