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3. Microbial influences on the resuspension and deposition processes of sediment transport

Author

Zhang, Naiyu and Thompson, Charlotte

Abstract

The extensive presence of microbial cells in aquatic sediments and the complex interactions/aggregations with sediment particles are found to have substantial effects on the dynamic processes of sediment transport. To date, extensive efforts have been paid to investigate such complex but typically common processes, but we are still far from a clear understanding. Specifically, the three-dimensional (3D) matrices of biosediment association, microbial mediation in the enhancement and reduction of sediment stability, and the effects of bio-sediment association on drag and settling velocities, remain to be clearly understood. This thesis seeks for a clearer and more comprehensive understanding of microbial sediment interactions and the influences on the resuspension and deposition processes of sediment transport. To achieve these goals, a new approach has been developed by using X-ray microtomography techniques, which for the first time allows the 3D matrices of biological sediment aggregates (BSA) to be imaged and quantified in their hydrated states. The results show that the microbial development state and the complex microbial sediment interaction/aggregation can significantly affect BSA architectures. As the BSA grow towards a better developed state, with higher organic fractions and larger aggregated sizes, the internal structure of BSA appears to become more compact and interconnected. The BSA at different stages of development in turn have a range of effects on sediment stability. The more fully developed BSA of a high organic fraction are found to biostabilize sediments, while the BSA at a less well developed state with lower organic fractions considerably destabilize sediments. By contrast, the microbial influences on the depositional processes present different patterns, where the volume of pore water plays a more important role in determining settling velocities, compared to the organic matter. These important results reveal the mechanisms and properties that influence microbial moderations of resuspension and deposition processes, providing much needed insight into microbial sediment transport. Predictive relationships for estimating the stability, drag and settling velocities of BSA are also tentatively proposed based on the test data available. The insights gained suggest important possibilities for future work to achieve a more complete characterization of sediment transport in the presence of microbial mediation.

Published
2021

6. Phosphorus Distribution within Aggregates in Long-Term Fertilized Black Soil: Regulatory Mechanisms of Soil Organic Matter and pH as Key Impact Factors.

Author

Zhang, Naiyu, Wang, Qiong, Chen, Yanhua, Zhang, Shuxiang, Zhang, Xianmei, Feng, Gu, Gao, Hongjun, Peng, Chang, and Zhu, Ping

Subjects
*BLACK cotton soil, *SOIL structure, *ORGANIC compounds, *PHOSPHORUS in soils, *SOIL acidity, *POTASSIUM
Abstract

Understanding soil phosphorus (P) distribution and its key drivers is fundamental for sustainable P management. In this study, a 21-year fertilization experiment on black soil was carried out, setting up five fertilization treatments: unfertilized control (CK), nitrogen and potassium (NK), nitrogen, P and potassium (NPK), NPK plus straw (NPKS), and NPK plus manure (NPKM). The distribution and effecting factors of P pools within soil aggregates were investigated. Compared to CK, the NK and NPK treatments decreased calcium-associated P concentration in all aggregate fractions. Meanwhile, the NPK treatment significantly increased the organic P extracted from NaOH in unaggregated particles (<0.053 mm). This was mainly due to the reduction in soil pH. The NPKS and NPKM treatments increased almost all P forms in aggregates, especially Ca-P. For the NPKM treatment, inorganic P extracted from resin, NaHCO3, and NaOH increased as aggregate size increased. This was mainly because straw or manure addition promoted soil organic carbon (SOC) storage in aggregates, creating more sorption sites via association with amorphous metallic minerals, and, thus, facilitating P accumulation. In conclusion, decreasing soil pH by chemical fertilizers is an effective strategy for mobilizing soil P, whereas increasing SOC by straw or manure facilitates P accumulation. [ABSTRACT FROM AUTHOR]

Published
2024
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8. The Genome-Wide Identification, Characterization, and Expression Profiles of the NADPH Oxidase (NOX) Gene Family under Drought and Salt Stress in Opisthopappus taihangensis (Asteraceae).

Author

Ye, Hang, Liu, Hengzhao, Han, Mian, Zhang, Naiyu, Feng, Xiaolong, Gao, Ting, Lei, Dingfan, Li, Haochen, Gao, Zhimei, Su, Yu, Chai, Min, Zhou, Huijuan, and Wang, Yiling

Subjects
GENE families, NADPH oxidase, GENE expression, ASTERACEAE, DROUGHTS, GERMPLASM
Abstract

Plant NAPDH oxidase (NOX) gene family members are critical producers of ROS and play crucial roles in plant signaling, development, and stress responses. Opisthopappus taihangensis is a pivotal wild genetic resource in Asteraceae. To date, little knowledge exists about the functions of NOXs in O. taihangensis. In this study, seven typical NOXs and seven ferric reduction oxidases (FROs) were identified in O. taihangensis. Dispersed duplication might play a critical role in the expansion of the NOX/FRO gene family in O. taihangensis, and most of the NOX/FRO homologous pairs have undergone purifying selection. Although the results of the collinearity analysis show that these genes were relatively conserved, the gain and loss of members in this gene family occurred frequently during the evolution of Asteraceae. Phylogenetic analysis indicated that the FROs are relatively ancient, and the earliest diverged branch was revealed by the maximum likelihood (ML) tree. The Asteraceae NOXs were divided into six subgroups according to their relationship with Arabidopsis and rice members. The transcriptome profile unveiled tissue-specific expression patterns and complex response modes under drought and salt stresses. OtNOX6 and OtNOX7 could be recognized as important candidates to respond to drought and salt stress. Our results provide clues and references for further in-depth exploration of NOX/FRO function in O. taihangensis and other horticulture plants. [ABSTRACT FROM AUTHOR]

Published
2024
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14. Quantitative Evaluation of the Crop Yield, Soil-Available Phosphorus, and Total Phosphorus Leaching Caused by Phosphorus Fertilization: A Meta-Analysis.

Author

Jin, Yuwen, Zhang, Naiyu, Chen, Yanhua, Wang, Qiong, Qin, Zhenhan, Sun, Zhimei, and Zhang, Shuxiang

Subjects
*CROP yields, *PHOSPHATE fertilizers, *LEACHING, *SOIL fertility, *SOIL density
Abstract

Phosphorus (P) leaching from excessive P application is the primary pathway of P losses in agricultural soils. Different P fertilizer practices have mixed effects on P leaching. We conducted a meta-analysis of the relevant literature regarding the response of crop yields, soil-available P (AP), and total P (TP) leaching to reduced P input (RP) and an inorganic-organic combination fertilizer (NPKM) for different agricultural land-use types. Compared to conventional P application (CP), RP (10~90% reduction) did not reduce crop yields in vegetable fields (experiments were 1~4 years) but significantly reduced cereal yields by 4.57%. Compared to chemical fertilizer (NPK), NPKM significantly increased cereal yields by 12.73%. Compared to CP, RP significantly reduced AP at 0~60 cm in vegetable and cereal fields. The greatest reduction occurred at 20~40 cm in vegetable fields (40.29%) and 0~20 cm in cereal fields (34.45%). Compared to NPK, NPKM significantly increased the AP at 0~60 cm in vegetable fields, with the greatest increase (52.44%) at 20~40 cm. The AP at 0~40 cm in cereal fields significantly increased under the NPKM treatment, with the greatest increase at 0~20 cm (76.72%). Compared to CP, RP significantly decreased TP leaching by 16.02% and 31.50% in vegetable and cereal fields, respectively. Compared to NPK, NPKM significantly increased TP leaching in vegetable fields (30.43%); no significant difference in leaching occurred in cereal fields. P leaching, in response to RP, was influenced by the P amounts applied (34.49%); soil organic matter (14.49%); and TP (12.12%). P leaching in response to NPKM was influenced by multiple factors: rainfall (16.05%); soil organic matter (12.37%); soil bulk density (12.07%); TP (11.65%); pH (11.41%). NPKM was more beneficial for improving yields in cereal fields with low soil fertility and lower P-leaching risks. [ABSTRACT FROM AUTHOR]

Published
2023
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18. A Massive Parallel Cellular GPU Implementation of Neural Network to Large Scale Euclidean TSP

Author

Wang, Hongjian, Zhang, Naiyu, Créput, Jean-Charles, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Doug, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Goebel, Randy, editor, Siekmann, Jörg, editor, Wahlster, Wolfgang, editor, Castro, Félix, editor, Gelbukh, Alexander, editor, and González, Miguel, editor

Published
2013
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25. A study of the application potential of I-Kr models based on the influencing effects of shaly sandstone reservoirs.

Author

Pan, BaoZhi, Zhang, PengJi, Guo, YuHang, Zhang, LiHua, Wang, XinRu, and Zhang, NaiYu

Abstract

Relative permeability is one of the important parameters for reservoir interpretation and productivity prediction. The main methods used to obtain the relative permeability in the laboratory are the steady-state method and unsteady-state method, but both of these are relatively expensive and require long preparation times. Many researchers try to infer the relative permeability curve from other petrophysical parameters. The most representative one is the method used to calculate the relative permeability of the wetting and non-wetting phases according to the resistivity index I. In previous studies, the existing I-Kr models, such as the Li model and Ma model, have been generally effective in sandstone reservoir, yet not as effective in shaly sandstone reservoirs. In this study, in order to solve the problem of low productivity prediction accuracy caused by the complex oil-water relationship in the shaly sandstone reservoirs in the Xujiaweizi area of Daqing, it is necessary to establish a suitable I-Kr model for the shaly sandstone reservoirs in this area. Based on the improved W-S model, the resistivity index I* and its calculation equation are established to eliminate the influence of the additional conductivity of shale. This resistivity index I* is able to more accurately reflect the conductivity of the shaly sandstone reservoirs; thus a new I*-Kr* model of shaly sandstone reservoirs is successfully established by introducing the modification term of wetting phase relative permeability. In addition, for the shaly sandstone reservoirs, a working process is also proposed, which could be applied to wells in the study area. In order to verify the new model, the productivity prediction and reservoir evaluation were carried out for two sections of a well in this area. The comparison between the productivity calculation results and the actual oil test results proves the accuracy and applicability of the I*-Kr* model in this paper, which effectively improved the accuracy of shaly sandstone reservoir interpretation and productivity prediction. [ABSTRACT FROM AUTHOR]

Published
2021
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29. Cellular GPU Models to Euclidean Optimization Problems : Applications from Stereo Matching to Structured Adaptive Meshing and Traveling Salesman Problem

Author

Zhang, Naiyu and STAR, ABES

Subjects
Maillage adaptatif, 3d reconstruction, Combinatorial optimization, Reconstruction 3D, GPU, Stereovision, Stéréo-vision, Multi-processeurs, Traveling salesman problem, [INFO.INFO-CY] Computer Science [cs]/Computers and Society [cs.CY], Problème du voyageur de commerce, Adaptive meshing, Multiprocessors, Graphics Processing Units, Optimisation combinatoire
Abstract

The work presented in this PhD studies and proposes cellular computation parallel models able to address different types of NP-hard optimization problems defined in the Euclidean space, and their implementation on the Graphics Processing Unit (GPU) platform. The goal is to allow both dealing with large size problems and provide substantial acceleration factors by massive parallelism. The field of applications concerns vehicle embedded systems for stereovision as well as transportation problems in the plane, as vehicle routing problems. The main characteristic of the cellular model is that it decomposes the plane into an appropriate number of cellular units, each responsible of a constant part of the input data, and such that each cell corresponds to a single processing unit. Hence, the number of processing units and required memory are with linear increasing relationship to the optimization problem size, which makes the model able to deal with very large size problems.The effectiveness of the proposed cellular models has been tested on the GPU parallel platform on four applications. The first application is a stereo-matching problem. It concerns color stereovision. The problem input is a stereo image pair, and the output a disparity map that represents depths in the 3D scene. The goal is to implement and compare GPU/CPU winner-takes-all local dense stereo-matching methods dealing with CFA (color filter array) image pairs. The second application focuses on the possible GPU improvements able to reach near real-time stereo-matching computation. The third and fourth applications deal with a cellular GPU implementation of the self-organizing map neural network in the plane. The third application concerns structured mesh generation according to the disparity map to allow 3D surface compressed representation. Then, the fourth application is to address large size Euclidean traveling salesman problems (TSP) with up to 33708 cities.In all applications, GPU implementations allow substantial acceleration factors over CPU versions, as the problem size increases and for similar or higher quality results. The GPU speedup factor over CPU was of 20 times faster for the CFA image pairs, but GPU computation time is about 0.2s for a small image pair from Middlebury database. The near real-time stereovision algorithm takes about 0.017s for a small image pair, which is one of the fastest records in the Middlebury benchmark with moderate quality. The structured mesh generation is evaluated on Middlebury data set to gauge the GPU acceleration factor and quality obtained. The acceleration factor for the GPU parallel self-organizing map over the CPU version, on the largest TSP problem with 33708 cities, is of 30 times faster., Le travail présenté dans ce mémoire étudie et propose des modèles de calcul parallèles de type cellulaire pour traiter différents problèmes d’optimisation NP-durs définis dans l’espace euclidien, et leur implantation sur des processeurs graphiques multi-fonction (Graphics Processing Unit; GPU). Le but est de pouvoir traiter des problèmes de grande taille tout en permettant des facteurs d’accélération substantiels à l’aide du parallélisme massif. Les champs d’application visés concernent les systèmes embarqués pour la stéréovision de même que les problèmes de transports définis dans le plan, tels que les problèmes de tournées de véhicules. La principale caractéristique du modèle cellulaire est qu’il est fondé sur une décomposition du plan en un nombre approprié de cellules, chacune comportant une part constante de la donnée, et chacune correspondant à une unité de calcul (processus). Ainsi, le nombre de processus parallèles et la taille mémoire nécessaire sont en relation linéaire avec la taille du problème d’optimisation, ce qui permet de traiter des instances de très grandes tailles.L’efficacité des modèles cellulaires proposés a été testée sur plateforme parallèle GPU sur quatre applications. La première application est un problème d’appariement d’images stéréo. Elle concerne la stéréovision couleur. L’entrée du problème est une paire d’images stéréo, et la sortie une carte de disparités représentant les profondeurs dans la scène 3D. Le but est de comparer des méthodes d’appariement local selon l’approche winner-takes-all et appliquées à des paires d’images CFA (color filter array). La deuxième application concerne la recherche d’améliorations de l’implantation GPU permettant de réaliser un calcul quasi temps-réel de l’appariement. Les troisième et quatrième applications ont trait à l’implantation cellulaire GPU des réseaux neuronaux de type carte auto-organisatrice dans le plan. La troisième application concerne la génération de maillages structurés appliquée aux cartes de disparité afin de produire des représentations compressées des surfaces 3D. Enfin, la quatrième application concerne le traitement d’instances de grandes tailles du problème du voyageur de commerce euclidien comportant jusqu’à 33708 villes.Pour chacune des applications, les implantations GPU permettent une accélération substantielle du calcul par rapport aux versions CPU, pour des tailles croissantes des problèmes et pour une qualité de résultat obtenue similaire ou supérieure. Le facteur d’accélération GPU par rapport à la version CPU est d’environ 20 fois plus vite pour la version GPU sur le traitement des images CFA, cependant que le temps de traitement GPU est d’environ de 0,2s pour une paire d’images de petites tailles de la base Middlebury. L’algorithme amélioré quasi temps-réel nécessite environ 0,017s pour traiter une paire d’images de petites tailles, ce qui correspond aux temps d’exécution parmi les plus rapides de la base Middlebury pour une qualité de résultat modérée. La génération de maillages structurés est évaluée sur la base Middlebury afin de déterminer les facteurs d’accélération et qualité de résultats obtenus. Le facteur d’accélération obtenu pour l’implantation parallèle des cartes auto-organisatrices appliquée au problème du voyageur de commerce et pour l’instance avec 33708 villes est de 30 pour la version parallèle.

Published
2013

30. Modèles cellulaires GPU appliquès à des problèmes d'optimisation euclidiennes : applications à l'appariement d'images stéréo, à la génération de maillages et au voyageur de commerce

Author

Zhang, Naiyu and STAR, ABES

Subjects
Maillage adaptatif, 3d reconstruction, Combinatorial optimization, Reconstruction 3D, GPU, Stereovision, Stéréo-vision, Multi-processeurs, Traveling salesman problem, [INFO.INFO-CY] Computer Science [cs]/Computers and Society [cs.CY], Problème du voyageur de commerce, Adaptive meshing, Multiprocessors, Graphics Processing Units, Optimisation combinatoire
Abstract

The work presented in this PhD studies and proposes cellular computation parallel models able to address different types of NP-hard optimization problems defined in the Euclidean space, and their implementation on the Graphics Processing Unit (GPU) platform. The goal is to allow both dealing with large size problems and provide substantial acceleration factors by massive parallelism. The field of applications concerns vehicle embedded systems for stereovision as well as transportation problems in the plane, as vehicle routing problems. The main characteristic of the cellular model is that it decomposes the plane into an appropriate number of cellular units, each responsible of a constant part of the input data, and such that each cell corresponds to a single processing unit. Hence, the number of processing units and required memory are with linear increasing relationship to the optimization problem size, which makes the model able to deal with very large size problems.The effectiveness of the proposed cellular models has been tested on the GPU parallel platform on four applications. The first application is a stereo-matching problem. It concerns color stereovision. The problem input is a stereo image pair, and the output a disparity map that represents depths in the 3D scene. The goal is to implement and compare GPU/CPU winner-takes-all local dense stereo-matching methods dealing with CFA (color filter array) image pairs. The second application focuses on the possible GPU improvements able to reach near real-time stereo-matching computation. The third and fourth applications deal with a cellular GPU implementation of the self-organizing map neural network in the plane. The third application concerns structured mesh generation according to the disparity map to allow 3D surface compressed representation. Then, the fourth application is to address large size Euclidean traveling salesman problems (TSP) with up to 33708 cities.In all applications, GPU implementations allow substantial acceleration factors over CPU versions, as the problem size increases and for similar or higher quality results. The GPU speedup factor over CPU was of 20 times faster for the CFA image pairs, but GPU computation time is about 0.2s for a small image pair from Middlebury database. The near real-time stereovision algorithm takes about 0.017s for a small image pair, which is one of the fastest records in the Middlebury benchmark with moderate quality. The structured mesh generation is evaluated on Middlebury data set to gauge the GPU acceleration factor and quality obtained. The acceleration factor for the GPU parallel self-organizing map over the CPU version, on the largest TSP problem with 33708 cities, is of 30 times faster., Le travail présenté dans ce mémoire étudie et propose des modèles de calcul parallèles de type cellulaire pour traiter différents problèmes d’optimisation NP-durs définis dans l’espace euclidien, et leur implantation sur des processeurs graphiques multi-fonction (Graphics Processing Unit; GPU). Le but est de pouvoir traiter des problèmes de grande taille tout en permettant des facteurs d’accélération substantiels à l’aide du parallélisme massif. Les champs d’application visés concernent les systèmes embarqués pour la stéréovision de même que les problèmes de transports définis dans le plan, tels que les problèmes de tournées de véhicules. La principale caractéristique du modèle cellulaire est qu’il est fondé sur une décomposition du plan en un nombre approprié de cellules, chacune comportant une part constante de la donnée, et chacune correspondant à une unité de calcul (processus). Ainsi, le nombre de processus parallèles et la taille mémoire nécessaire sont en relation linéaire avec la taille du problème d’optimisation, ce qui permet de traiter des instances de très grandes tailles.L’efficacité des modèles cellulaires proposés a été testée sur plateforme parallèle GPU sur quatre applications. La première application est un problème d’appariement d’images stéréo. Elle concerne la stéréovision couleur. L’entrée du problème est une paire d’images stéréo, et la sortie une carte de disparités représentant les profondeurs dans la scène 3D. Le but est de comparer des méthodes d’appariement local selon l’approche winner-takes-all et appliquées à des paires d’images CFA (color filter array). La deuxième application concerne la recherche d’améliorations de l’implantation GPU permettant de réaliser un calcul quasi temps-réel de l’appariement. Les troisième et quatrième applications ont trait à l’implantation cellulaire GPU des réseaux neuronaux de type carte auto-organisatrice dans le plan. La troisième application concerne la génération de maillages structurés appliquée aux cartes de disparité afin de produire des représentations compressées des surfaces 3D. Enfin, la quatrième application concerne le traitement d’instances de grandes tailles du problème du voyageur de commerce euclidien comportant jusqu’à 33708 villes.Pour chacune des applications, les implantations GPU permettent une accélération substantielle du calcul par rapport aux versions CPU, pour des tailles croissantes des problèmes et pour une qualité de résultat obtenue similaire ou supérieure. Le facteur d’accélération GPU par rapport à la version CPU est d’environ 20 fois plus vite pour la version GPU sur le traitement des images CFA, cependant que le temps de traitement GPU est d’environ de 0,2s pour une paire d’images de petites tailles de la base Middlebury. L’algorithme amélioré quasi temps-réel nécessite environ 0,017s pour traiter une paire d’images de petites tailles, ce qui correspond aux temps d’exécution parmi les plus rapides de la base Middlebury pour une qualité de résultat modérée. La génération de maillages structurés est évaluée sur la base Middlebury afin de déterminer les facteurs d’accélération et qualité de résultats obtenus. Le facteur d’accélération obtenu pour l’implantation parallèle des cartes auto-organisatrices appliquée au problème du voyageur de commerce et pour l’instance avec 33708 villes est de 30 pour la version parallèle.

Published
2013

31. A Near Real-Time Color Stereo Matching Method for GPU

Author

Zhang, Naiyu, Wang, Hongjian, Creput, Jean-Charles, Moreau, Julien, Ruichek, Yassine, and Moreau, Julien

Subjects
[INFO.INFO-CV] Computer Science [cs]/Computer Vision and Pattern Recognition [cs.CV], [INFO.INFO-DC] Computer Science [cs]/Distributed, Parallel, and Cluster Computing [cs.DC], [INFO] Computer Science [cs], ComputingMilieux_MISCELLANEOUS
Published
2013

32. Partial Demosaicing for stereo matching of CFA images on GPU and CPU

Author

Zhang, Naiyu, Creput, Jean-Charles, Wang, Hongjian, Meurie, Cyril, Ruichek, Yassine, and Cadic, Ifsttar

Subjects
[INFO.INFO-TS] Computer Science [cs]/Signal and Image Processing, Computer Science::Computer Vision and Pattern Recognition, VISION ARTIFICIELLE, TRAITEMENT DES IMAGES, [SPI.SIGNAL] Engineering Sciences [physics]/Signal and Image processing
Abstract

This paper presents a GPU implementation of a partial demosaicing scheme that is specially designed for stereo matching of CFA image. This method consists of three main techniques keys: the adapted matching cost for CFA image, the estimated Second color component based on Hamilton’s estimate method and a robust cost aggregation window. Experiments are carried out to explore the performance for this method on GPU both at matching quality and matching efficiency, with comparison with version on CPU. The experiments on different size image pairs from Middlebury dataset show that this method can be substantially accelerated on GPU when the image size is large and has still space for improvements in performance.

Published
2013

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