Result of the soil chemical analysis on the 11 locations in the Philippines.
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More than half of the publishers listed alongside IntechOpen (18 out of 30) are Social Science and Humanities publishers. IntechOpen is an exception to this as a leader in not only Open Access content but Open Access content across all scientific disciplines, including Physical Sciences, Engineering and Technology, Health Sciences, Life Science, and Social Sciences and Humanities.
\\n\\nOur breakdown of titles published demonstrates this with 47% PET, 31% HS, 18% LS, and 4% SSH books published.
\\n\\n“Even though ItechOpen has shown the potential of sci-tech books using an OA approach,” other publishers “have shown little interest in OA books.”
\\n\\nAdditionally, each book published by IntechOpen contains original content and research findings.
\\n\\nWe are honored to be among such prestigious publishers and we hope to continue to spearhead that growth in our quest to promote Open Access as a true pioneer in OA book publishing.
\\n\\n\\n\\n
\\n"}]',published:!0,mainMedia:null},components:[{type:"htmlEditorComponent",content:'
Simba Information has released its Open Access Book Publishing 2020 - 2024 report and has again identified IntechOpen as the world’s largest Open Access book publisher by title count.
\n\nSimba Information is a leading provider for market intelligence and forecasts in the media and publishing industry. The report, published every year, provides an overview and financial outlook for the global professional e-book publishing market.
\n\nIntechOpen, De Gruyter, and Frontiers are the largest OA book publishers by title count, with IntechOpen coming in at first place with 5,101 OA books published, a good 1,782 titles ahead of the nearest competitor.
\n\nSince the first Open Access Book Publishing report published in 2016, IntechOpen has held the top stop each year.
\n\n\n\nMore than half of the publishers listed alongside IntechOpen (18 out of 30) are Social Science and Humanities publishers. IntechOpen is an exception to this as a leader in not only Open Access content but Open Access content across all scientific disciplines, including Physical Sciences, Engineering and Technology, Health Sciences, Life Science, and Social Sciences and Humanities.
\n\nOur breakdown of titles published demonstrates this with 47% PET, 31% HS, 18% LS, and 4% SSH books published.
\n\n“Even though ItechOpen has shown the potential of sci-tech books using an OA approach,” other publishers “have shown little interest in OA books.”
\n\nAdditionally, each book published by IntechOpen contains original content and research findings.
\n\nWe are honored to be among such prestigious publishers and we hope to continue to spearhead that growth in our quest to promote Open Access as a true pioneer in OA book publishing.
\n\n\n\n
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The effective management of many aquatic environments, requires a detailed understanding of sediment dynamics. This has both environmental and economic implications, especially where there is any anthropogenic involvement. Numerical models are often the tool used for predicting the transport and fate of sediment movement in these situations, as they can estimate the various spatial and temporal fluxes. However, the physical sedimentary processes can vary quite considerably depending upon whether the local sediments are fully cohesive, non-cohesive, or a mixture of both types. For this reason for more than half a century, scientists, engineers, hydrologists and mathematicians have all been continuing to conduct research into the many aspects which influence sediment transport. These issues range from processes such as erosion and deposition to how sediment process observations can be applied in sediment transport modeling frameworks. This book reports the findings from recent research in applied sediment transport which has been conducted in a wide range of aquatic environments. The research was carried out by researchers who specialize in the transport of sediments and related issues. I highly recommend this textbook to both scientists and engineers who deal with sediment transport issues.",isbn:null,printIsbn:"978-953-307-586-0",pdfIsbn:"978-953-51-4922-4",doi:"10.5772/827",price:139,priceEur:155,priceUsd:179,slug:"sediment-transport-in-aquatic-environments",numberOfPages:346,isOpenForSubmission:!1,isInWos:1,hash:"0eb11af1d03ad494253c41e1d3c998e9",bookSignature:"Andrew J. 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\r\n\tOrganic synthesis has always been one of the central topics of research for the scientific community in the academic laboratories and industrial world. Many striking journal articles and remarkable reviews and books have been published in the past year describing the practicability and applications of the subject demonstrating the importance of organic synthesis. In the present book, we will be putting together the topics in organic synthesis which may include but not limited to, (1) the basic terms and concepts, (2) various organic reactions including reduction, oxidation, addition, elimination, rearrangements, and cycloadditions, (3) Total Synthesis of Natural products, (4) transition metal catalysts, organocatalysts, enzymes and biotransformations, (5) applications in medicinal chemistry and drug design and development, (6) purification methods and characterization techniques, etc. To set a limit and to increase the scope of the book, author(s) are encouraged to send the chapters that include selected examples with practical applications and good yielding reactions reported within the past decade. Older topics with significant findings or their essence to prepare the foundation may be included in the chapter are welcomed as well.
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Deore was born in India. He received a Master’s degree in organic chemistry from Pune University in 2007. In the same year, he qualified with the SET and CSIR-NET (JRF) and joined in the group of Prof. Narshinha P. Argade for the doctoral studies in National Chemical Laboratory, India. In 2014, he awarded with a Ph. D. in Chemistry and was a recipient of the 2nd prize in “2014 Eli Lilly and Company Asia Outstanding Thesis Awards”. In July 2014 he moved to Canada and joined as a postdoctoral researcher in the group of Prof. Richard Manderville at the University of Guelph, Canada. Presently, Dr. Deore is working on the collaborative project between the University of Guelph and Aterica health Inc., and providing consulting to the company. 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Simulation of an entire system including both hardware and software from early design stages is one of the effective approaches to improve the design productivity. A large number of research effortson hardware/software (HW/SW) co-simulation have been made so far. Real-time operating systems have become one of the important components in the embedded systems. However, in order to validate function of the entire system, this system has to be simulated together with application software and hardware. Indeed, traditional methods of verification have proven to be insufficient for complex digital systems. Register transfer level test-benches have become too complex to manage and too slow to execute. New methods and verification techniques began to emerge over the past few years. High-level test-benches, assertion-based verification, formal methods, hardware verification languages are just a few examples of the intense research activities driving the verification domain.
Our work articulates on three contributions which arethe proposal for solutions to the implementation of the different parts of the architecture using SystemC andMatlab/Simulink simulators. Secondly, the definition of a co-simulation environment based on the automatic generation of the interfaces required to the integration of these simulators. Finally, the proposal of a new verification framework based on SystemC Verification standard that uses MATLAB/Simulink to accelerate the test-bench development. This chapter attempts to give a guide for the implementation of real-time control systems, using the S-function of matlab/Simulink, as a practical tool for students in control engineering.The MATLAB/Simulink to SystemC interface and the advanced version of transactors are combined in a scalable multi-abstraction level verification platform. The proposed refined co-simulation platform enables co-simulation with hardware models written in SystemC. On that platform, application software and hardware modules are directly executed on a host computer, which leads to a high co-simulation speed. The MATLAB/SystemC interface is mainly used for the verification of the lower abstraction levels with a high level model of theirexecution environment.
The integration of SystemC within MATLAB/Simulink and the resulting verification flow is tested on the JPEG compression algorithm. The required synchronization of both simulation environments, including data type conversion,is solved by using the proposed co-simulation flow. The application is divided into two JPEG encoder parts: the DCT (Direct Cosine Transform), the HW part implemented in SystemC, and the QEE (Quantization and Entropy Encoding),the SW part implemented in Matlab. With this research premise, this study introduces a new HW implementation of the DCT algorithm in SystemC. For the communication and synchronization between these two parts we use the S-Function and the MATLAB/Simulink engine. In addition, we compare the co-simulation results to a pure software simulation.
In this chapter, the related work is discussed in Section 2 and the proposed co-simulation methodology is presented in Section 3. Then, in Section 4, we propose the implementation of the JPEG image compression as a case study. We present the steps in matlab for the implementation of the JPEG algorithm. In Section 5,we summarize the proposed approach and co-simulation results. Finally, we sum up the proposal including suggestions and recommendations to future works.
First of all, we present the chosen two simulators: Matlab and SystemC.
The MATLAB environment is a high-level technical computing language for algorithm development, data visualization, data analysis and numerical computing. One of the key features of this tool is the integration ability with other languages and third-party applications. MATLAB also included the Simulink graphical environment used for multi-domain simulation and model-based design. Signal processing designers take advantage of Simulink as it offers a good platform for preliminary algorithmic exploration and optimization. A hardware designer doesn’t like C/C++ environment because of:
Concurrency support is missing (HW is inherently parallel)
No notion of time (clock, delays)
Communication model (function calls & parameters) is very different from actual HW model (pins & signals)
Weak/complex reactivity to events
Some data types missing (logic values, bit vectors, fixed point).
The resulting modelling language is System C.
Connecting Simulink and SystemC together have already been tried in the literature. Authors in [6] propose a solution to integrate SystemC models in Simulink. A wrapper is created using S-Functions to combine SystemC modules with Simulink.
This wrapper initializes the SystemC kernel and converts Simulink data type to SystemC signals and vice versa. Simulation control is entirely handled by Simulink. Some extensions of the SystemC kernel are required for initialization and simulation tasks. In [7], SystemC calls MATLAB using the engine library. MATLAB provides interfaces to external routines written in other programming languages. Using the C engine library, it is possible to share data between SystemC models and MATLAB. This simple working demo shows how to use the library to send, to retrieve data from the MATLAB workspace and to plot some results. The main difference with [6] is with the simulation control: SystemC is now the master of the simulation and MATLAB operates as a slave process. Also, Simulink is not supported in this example.
In a similar way, MathWorks provides a commercial solution to close the gap between the algorithmic domain and the hardware design. The link for ModelSim [8] is a co-simulation interface that integrates MATLAB and Simulink into the hardware design flow. It provides a link between MATLAB/Simulink and Model Technology’s HDL simulator, ModelSim. This interface makes the verification and co-simulation of RTL-level models possible from within MATLAB and Simulink. As opposed to the two previous techniques, there is no support for system level languages like SystemC.
These approaches [6, 7, 8] all try to reduce the barrier that exist between higher level modeling and existing hardware design flow. While [8] is a fully functional commercial tool for RTL verification, [6, 7] suffer from their embryonic stage (i.e. incomplete solutions for hardware design and verification).
The authors in [9] look at the problem of cosimulating continuous systems with discrete systems. The increasing complexity of continuous/discrete systems makes their simulation and validation a demanding task for the design of heterogeneous systems. They propose a co-simulation interface based on Simulink and SystemC. The main objective of the proposed solution is to provide a framework to evaluate continuous/discrete systems modeling and simulation.
In work [10], the authors have created a tool called: co-simulation COLIF that defines a subset of Matlab / simulink and combines a set of descriptive rules allows for the specification and functional validation efficient algorithms for the application. To reduce the "gap" between the functional model and architecture model in SystemC, they proposed a new intermediate transactional model in Simulink executable that combines both the algorithm and architecture in a single model representation. To validate their work, they applied to decoder MPEG Layer III. They found that the simulation model in Simulink is 50 times faster than the macro-level architecture. The difference is mainly due to the complexity of the description and details of the communication are present at the macro architecture.
In our former work [11], we adopted the methodology of communication and synchronization. To exchange data between a Simulink model and SystemC module, the co-simulation interface must integrate a bridge between the two simulators. This bridge is built with two Simulink S-Functions. An S-Function is a computer language description of a Simulink block. It uses syntax of call allowing us to interact with Simulink solvers. For our bridge, we create two C++ S-Functions.
The representation of simulation time differs significantly from SystemC and Matlab. SystemC is cycle-based simulator and simulation occurs at multiples of the SystemC resolution limit. The default time resolution is one picosecond. This limit can be changed with the function sc_set_time_resolution. However, Simulink maintains simulation time as a double precision value scaled to seconds. Thus, our co-simulation interface uses a one-to-one correspondence between simulation time in Simulink and SystemC.
The implementation of applications on embedded systems is a very time expensive task using the standard development tools. The proposed heterogeneous model is also executable to simulate the co-design implementation. Such simulation of the heterogeneous model is realized using SystemC. In fact, a description of a hardware module is transformed into a structural description with SystemC components (RT-level). Then, the interface between hardware and software parts is implemented using special SystemC constructs. This interface can be compared with the interface of the implementation in the real system. SystemC provides several levels of abstraction to describe hardware. For the simulation of hardware modules in the shown design flow given by figure Fig1, the cycle accurate level (CA) of SystemC is used. The interface to the software kernel is untimed functional level (UTF). A wrapper was designed to connect the modules to the software kernel. This wrapper is based on two shell-blocks which connect the CA-model to the software kernel by realizing an interface between the CA- and the UTF-model (Untimed Functional) of SystemC.
Simulink is a commonly used tool for designing DSP applications. It supports with a lot of libraries distinguished suppositions to develop single machine vision operators, e.g. the possibility to generate intelligent test environments for image. To use the tool for generation of hardware operators, an interface between SystemC and Simulink was developed. Thus, the visualized tool in more common design flows is integrated using Simulink S-Functions. Those Functions provide a powerful mechanism for extending Simulink with custom blocks and can be implemented as C++ Code. Within the S-Function the output is calculated from input and from states at each time step using a cycle by cycle SystemC-simulation as a fixed-step discrete time solver. The initialization of the SystemC kernel should be separated from simulation.
To meet these requirements a wrapper has been inserted between the S-Function and the SystemC model (Fig. 1). The wrapper functionalities are:
connecting Simulink ports to a SystemC-TM-Block,
converting Simulink data types to SystemC-TM signals and vice versa,
initializing of the SystemC-Kernel,
converting events; function call from Simulink to sc_cycle(),
providing a DLL interface to the Simulink S-Function.
Integrated SystemC in Simulink S-Function.
So, our methodology tries to push the idea a step further than just a co-simulation interface. It is a complete verification solution. It uses MATLAB external interfaces, similar to the example described in [6], to exchange data between SystemC and Simulink. Once this link is established, it opens up a wide range of additional capability to SystemC, like stimulus generation and data visualization[10]. We also based our methodology on a portion of the methodology in the work [11]. In this work, they are based on the transformation of a task in SystemC. The first advantage of our technique is to use the right tool for the right task. Complex stimulus generation and signal processing visualization are carried out with MATLAB and Simulink while hardware verification is performed with SystemC verification standard. The second advantage is to have a SystemC centric approach allowing greater flexibility and configurability.
With this approach the overall system simulation can be controlled by Simulink through settings of duration time and step size.
There are three new call-backs provided via virtual methods for classes derived from sc_module, sc_port, sc_export, and sc_prim_channel. These call-backs will be invoked by the SystemC simulation kernel when certain phases of the simulation process occur. The new methods are:
void before_end_of_elaboration();
This method is called just before the end of elaboration processing is to be done by the simulator.
void start_of_simulation();
This method is called just before the start of simulation. It is intended to allow users to set up variable traces and other verification functions that should be done at the start of simulation.
void end_of_simulation();
If a call to sc_stop() had been made this method will be called as part of the clean up process as the simulation ends. It is intended to allow users to perform final outputs, close files, storage, etc.
It is also possible to test whether the callbacks to the start_of_simulation methods or end_of_simulation methods have occurred. The Boolean functions sc_start_of_simulation_invoked() and sc_end_of_simulation_invoked() will return true if their respective callbacks have occurred.
The tasks at the transactional level under Simulink are included in a software knot represented by a sub-system having the prefix \' SW_ \' in its name. These tasks are modelled under Simulink in several ways.
They can be trained by a merger of several blocks in one under system having the name preceded by the prefix \' TASK _ \' either they are trained by individual blocks. These last ones, in turn can be predefined blocks of the library either Functions modelled in language C.
In what follows, the modelling of the tasks in SystemC will be explained before describing the various manners admitted to transform the tasks of transactional Simulink into tasks described in SystemC.
For the modelling and description of the tasks in SystemC, we used the notion of "SC_MODULE". A module can be hierarchical containing the other modules, or elementary containing an active or passive behaviour usingthe elementary modules "SC_CTHREAD". On the other hand, the communication is determined through an interface of communication. This last one is described through a set of ports which can be inputs, output orinputs / output ones. SystemC also supplies a specific portfor the modelling of a physical clock. The figure 2 shows the header file of a task described in SystemC. The interface of thismodule is formed by an input port and an output port of type \'long int\'. The task has aservice port \'SAP\', which allows synchronization of tasks in the co-simulation.
Example of a file header. "h" has a corresponding TASK SystemC.
However, the figure 3shows the main file. "cpp \'. The main calculation is done to the body of this task. The communication of this module with the system is through the interfaces represented by the ports of entry and exit \'DATA_IN1\'and \'DATA_OUT1\' by means of APIs defined in the library.
Example of a file header. "cpp" has a corresponding task SystemC.
SystemC is used by the synthesis tools and co-simulation in the stream of conception flow of the proposed heterogeneous Systems. The conception process always begins with the specification of the application in the Simulink environment using S-Functions blocks. The S-Functions are developed in language C according to precise rules and through methods decided by the Simulinksimulator. An S-Function is formed by four essential methods. In our work, a blockS-Function will be converted in a module in SystemC trained by a \' thread \' sensitive to a signal \' SAP \'. The file S-function C will be processed in a direct manner in a header file and theimplementation file in C + +. To understand better the transformation of one S-Function into a task,we divided into four parts.
In the first part, we define global variables and we include the header files. \'H\'.S-function: header files of the library of Simulink (Simstruct.h...) macros, header files of the code, and global variables are defined.SystemC: The header files of the SystemC library, macros, code header files and global variables are defined.
In the second part, the initialization of variables and definition of input ports and output are included in this section.S-function: This part is formed by the method mdlInitializeSizes (SimStruct * S) where variables are initialized, and the number and size of ports of entry and exit are defined. SystemC: This part is divided on the header file and implementation file for SystemC. In the first type of port is defined. In the second module ports are declared and initialized. The type of the port depends on the type of communication used by the port (Shared memory, FIFO, signal synchronization).
In the third part, the APIs and the communication are the main calculation developed in this part along a loop that is repeated several times. S-function: Method mdloutput (SimStruct *S) is used in this part. The main calculation of the block is made. The data to be transmitted are affected ports by using the operator "=". This is a communication primitive. SystemC: The loop for (;;) in the implementation file contains the main calculation module. The calculation code in C is similar to that of the S-function.
The difference in this part occurs at the level of communication primitives. In S-function, a reading and writing data port is through the assignment operator "=".In SystemC there are two types of communication primitives:
The Get () and Put () to communicate through a FIFO.
The operator "=" to read and write to shared memory.
In the final part,there is the last part that runs at the end of the simulation.S-function: This part is formed by the method mdlterminate (SimStruct * S). SystemC: This part is after the end of the loop for (;;) of Part III and the end of the module.
In the case of an elementary block a different type of S-function included in a software node (a subsystem with the prefix \'SW_\'), the generation of the tasks SystemC is made from a bookshop of functions describing the behaviour of all the blocks Simulink used in theapplication.
Each function has the same name as the Simulink block and the corresponding module in our methodology. However, reading and writing data are specific through the APIs to each communication protocol. These APIs exist in the communication library. The type of communication protocol is identified in the \'Port\' of each module in our methodology. Figure 4 shows the generation of a task in SystemC from an individual block inSimulinktransaction, this block is transformed into a parameterized module under ourmethodology.
Generating a task from a basic block.
In the case where several units are grouped in a subsystem representing a task whose name is prefixed with \'TASK_’ the generation of the task SystemC is by assembling several library functions into a single task SystemC. Functions have the same names of the blocks. These functions exchange data via common variables. Communication with the system \'inter_Thread\' is via the APIs generated following the protocol communication defined in our methodology.
Figure 5 illustrates the merger of several blocks in Simulink transactional to generate a task in SystemC. The functions of the library F0 (), F1 () have the same names as the blocks F0, F1. The generation of APIs is done by identifying the type of protocol in each port of the module in the virtual architecture of our methodology.
Generating a task from a set of blocks in Simulink.
The baseline JPEG compression algorithm is the most basic form of sequential DCT based compression [12]. The process of JPEG-based encoding and decoding of images vary according to colordepth (8, 24 or 32 bits). However, the basic ideology for all color depths is same. The bitmap image stores raw pixel-by-pixel color values. In addition, 54 bytes are stored at the start of file as header information that includes image width and height, image file size, image color depth, etc. These 54 bytes must be taken into account whenever working with the bitmap images. Following the 54-byte header, the bitmap image holds the color values of each pixel that varies for different color depths. For an 8-bit image, this is simply one byte (8-bits) per pixel and for a 32-bit image; they are 4 bytes per pixel. For 8-bit pixels, the pre-processing stage divides image data into 8x8 blocks that are shifted from unsigned integers with range [0, 28 – 1] to signed integers with a range of [–27, 27 – 1] and then individually compressed at the 8x8 block level. The compression process for each block goes through the following processes in addition to preprocessing.
Discrete Cosine Transform (DCT)
Quantization
Zigzag
Entropy Encoding (commonly Huffman)
Decompression is an inverse process that performs the individual inverse of all the aboveprocesses.
At the input to the encoder, source image samples are grouped into 8x8 blocks, shifted from unsigned integers with range [0, 27 - 1] to signed integers with range [-27-1, 27ˉ¹-1], and input to the Forward DCT (FDCT). At the output from the decoder, the Inverse DCT (IDCT) outputs 8x8 sample blocks to form the reconstructed image. The following equations are the idealized mathematical definitions of the 8x8 FDCT and 8x8 IDCT:
The DCT is related to the Discrete Fourier Transform (DFT). Some simple intuition for DCT-based compression can be obtained by viewing the FDCT as a harmonic analyzer and the IDCT as a harmonic synthesizer. Each 8x8 block of source image samples is effectively a 64-point discrete signal which is a function of the two spatial dimensions x and y. The FDCT takes such a signal as its input and decomposes it into 64 orthogonal basis signals. Each contains one of the 64 unique two-dimensional (2D) “spatial frequencies’’ which comprise the input signal’s “spectrum.” The ouput of the FDCT is the set of 64 basis-signal amplitudes or “DCT coefficients” whose values are uniquely determined by the particular64-point input signal.
The DCT coefficient values can thus be regarded as the relative amount of the 2D spatial frequencies contained in the 64-point input signal. The coefficient with zero frequency in both dimensions is called the “DC coefficient” and the remaining 63 coefficients are called the “AC coefficients.’’ Because sample values typically vary slowly from point to point across an image, the FDCT processing step lays the foundation for achieving data compression by concentrating most of the signal in the lower spatial frequencies. For a typical 8x8 sample block from a typical source image, most of the spatial frequencies have zero or near-zero amplitude and need not be encoded.
The JPEG decoder.
At the decoder the IDCT reverses this processing step. It takes the 64 DCT coefficients (which at that point have been quantized) and reconstructs a 64-point ouput image signal by summing the basis signals. Mathematically, the DCT is one-to-one mapping for 64-point vectors between the image and the frequency domains. If the FDCT and IDCT could be computed with perfect accuracy and if the DCT coefficients were not quantized as in the following description, the original 64-point signal could be exactly recovered. In principle, the DCT introduces no loss to the source image samples; it merely transforms them to a domain in which they can be more efficiently encoded. Some properties of practical FDCT and IDCT implementations raise the issue of what precisely should be required by the JPEG standard. A fundamental property is that the FDCT and IDCT equations contain transcendental functions.
After output from the FDCT, each of the 64 DCT coefficients is uniformly quantized in conjunction with a 64-element Quantization Table, which must be specified by the application (or user) as an input to the encoder. Each element can be any integer value from 1 to 255, which specifies the step size of the quantizer for its corresponding DCT coefficient. The purpose of quantization is to achieve further compression by representing DCT coefficients with no greater precision than is necessary to achieve the desired image quality. Stated another way, the goal of this processing step is to discard information which is not visually significant. Quantization is a many-to-one mapping, and therefore is fundamentally lossy. It is the principal source of lossiness in DCT-based encoders.
Quantization is defined as division of each DCT coefficient by its corresponding quantizer step size, followed by rounding to the nearest integer:
This output value is normalized by the quantizer step size. Dequantization is the inverse function, simply means in this casethat the normalization is removed by multiplying by the step size, which returns the result to a representation appropriate for input to the IDCT:
When the aim is to compress the image as much as possible without visible artifacts, each step size ideally should be chosen as the perceptual threshold or “just noticeable difference” for the visual contribution of its corresponding cosine basis function. These thresholds are also functions of the source image characteristics, display characteristics and viewing distance. For applications in which these variables can be reasonably well defined, psycho visual experiments can be performed to determine the best thresholds.
After quantization, the DC coefficient is treated separately from the 63 AC coefficients. The DC coefficient is a measure of the average value of the 64 image samples. Because there is usually strong correlation between the DC coefficients of adjacent 8x8 blocks, the quantized DC coefficient is encoded as the difference from the DC term of the previous block in the encoding order (defined in the following), as shown in Figure 7. This special treatment is worthwhile, as DC coefficients frequently contain a significant fraction of the total image energy.
Preparation of Quantized Coefficients for Entropy Coding
Finally, all of the quantized coefficients are ordered into the “zig-zag” sequence, also shown in Figure 7. This ordering helps to facilitate entropy coding by placing low-frequency coefficients (which are more likely to be nonzero) before high-frequency coefficients.
Huffman coding is a technique which will assign a variable length codeword toan input data item. Huffman coding assigns a smaller codeword to an input that occurs more frequently. It is very similar to Morse code, which assigned smaller pulse combinations to letters that occurred more frequently. Huffman coding is variable length coding, where characters are not coded to a fixed number of bits.
This is the last step in the encoding process. It organizes the data stream intoa smaller number of output data packets by assigning unique codewords that later during decompression can be reconstructed without loss. For the JPEG process, each combination of run length and size category, from the run length coder, are assigned a Huffman codeword.
It is possible to increase speed and to reduce power consumption by running portions of the algorithm implemented in the custom hardware. To do this, parts of the algorithm remains the SW and the other part goes to HW area and must be well chosen. This is called hardware partitioning software (HW / SW partitioning). Many factors must be considered when the HW / SW partitioning is done. The problem is to use the right amount of material. Using too much material implies a rise in costs and probably increase the time of placing on the market.
The first step in a HW / SW partitioning is to identify the parts of the algorithm that consumes a lot of time if left in the software or by the implementation of the algorithm entirely in software or perform estimates on the number of cycles. The next step is to evaluate and decide which parts need to be moved to the HW area. It is important to take into account more things than just a party that consumes more cycles of the software. Perhaps it is better to leave this part of computation in software intensiveand move some other parts in HW, the parts that are better suited for hardware implementation. This is of course possible only if time constraints may even now be suffering the most intense in the software calculation.
To make a good HW / SW partitioning a simulation tool is needed where much can be moved from HW field to SW field and vice versa. In addition, it should be possible to specify the execution time for different parts. This part of the design process is important and time spent here is well spent and often reduces the work in phases. If the processor architecture also must be chosen in the design process, the problem becomes even more complicated. With a more powerful processor, it is probably possible to do more in software and thus reduce the cost of designing and manufacturing the hardware. The question then is of course how this affects the total cost. The entire HW / SW partitioning problem is an optimization problem where constraints are typical on the surface of silicon, energy, monetary cost and execution time. So the time aspect of the market must be considered. In this section, we illustrate the approach we have followed for the implementation of JPEG through our methodology. As we have previously presented the most important part of the chain compression and DCT part, it has a lot of calculating. In this case we will implement this part with SystemC and the rest of the chain compression is implemented on MATLAB.
The following attempts to give a guide for the implementation ofthe JPEG compression algorithm in Figure 8.
Implementing the JPEG algorithm.
Matlab let us to choose the video when we click on the video source. A window is opened where we specify the video place and its parameter as it is presented in figure 9.
Choosing the video.
A click on the Block Profession opens window. In this window, there are the parameters of this block as a number of input, in our case, we put 1, number of output, in our case, we put 2 and two parameters are block size and overlap. A click the open Subsystem opens another window opens in which we find the block that we have just parameterize as indicated in figure 10.
Parameter of Block Processing.
Figure 11 below, shows the different parts of the implementation of the JPEG encoder.
Implementing the JPEG algorithm.
As motion in the chair, the DCT is the most important and contains much of calculation. This part of the chain will be developed in SystemC, and represents the Hardware part. We explain it using an exampleprocess named ‘DCT’ (in JPEG encoder) in SystemC as shown in Figure 12.
The DCT in SystemC.
It has twoFIFO channels, one for receiving data and the other for sending data. From the SystemC code, we remove all SystemC dependent statements and exchange the FIFO read/write.
TwoFIFO channels.
To proceed to an FPGA implementation, the resulting netlist from the previous stage has to be mapped to the FGPA\'s logic block structure and interconnect. The main outcome of this technology mapping, placing, and routing is a bit stream which can be programmed into a FPGA figure 13.
The virtual architecture model is described using SystemC language and is generated according to the parameters specified in the initial Simulink model. SystemC allows modeling a system at different abstraction levels from functional to pin accurate register transfer level.
The virtual architecture is modeled using transaction level modeling (TLM) techniques that allow analyzing FPGA architecture in an earlier phase of design, software development and timing estimation. At the virtual architecture level, the Simulink functions of the application are transformed into systemC program code for each task. This step is very similar to the code generation performed by Real Time Workshop (RTW).
Contrary to the RTW which generates only single task code, the software at the virtual architecture level represents a multitasking systemC code description of the initial Simulink application model. The generation has to support also user defined systemC codes integrated in the Simulink model as S-functions. For the S-functions, the task code represents a function call of the user written systemC function. The semantics of the argument passing are identical to those of the definition in the configuration panel of the S-Function Builder tool in Simulink. The hardware is refined to a set of abstract SystemC modules (SC_MODULE) for each subsystem. The SC_MODULE of the processor includes the tasks modules that are mapped on the processor and the communication channels for the intra-subsystem communication between the tasks inside the same processor. The communication channels between the tasks mapped on the FPGA is implemented using standard SystemC channels. The tasks modules are implemented as SystemC modules (SC_MODULE). The development of the JPEG Decoder application in Simulinkrequires 7 S-Functions in order to integrate the systemC code of the main parts of the decodingalgorithm.Which are: jpeg_sfun_h, dct_sfun_h,sfc_sf.h, sfc_mex.h, sfcdebug.h, jpeg_sfun.mexw32, dct_sfun.mexw32.
Once this link is established, it opens up a wide range of additional capability to SystemC, like stimulus generation and data visualization. The first advantage of our technique is to use the right tool for the right task. Complex stimulus generation and signal processing visualization are carried out with MATLAB and Simulink while hardware verification is performed with SystemC verification standard. The second advantage is to have a SystemC centric approach allowing greater flexibility and configurability.
In this part, we make a comparison between the previous methodology based on the communication and the synchronization between both simulators and the new approach which is based on the integration of systemC in matlab / Simulink in other applications.
CODIS (COntinuous DIscrete Simulation) is a tool which can automatically produces co-simulation instances for continuous/discrete systems simulation using SystemC and Simulink simulators. This is done by generating and providing co-simulation interfaces and the co-simulation bus. To evaluate the performances of simulation models generated in CODIS, they measured the overhead given by the simulation interfaces. The experiments have shown synchronization overhead of less than 30 % in simulation time [9]. In the [5] A Software-Defined Radio (SDR) is a combination of digital filters, analog components and processors, each requiring different design approaches with a different tool or language. Using a traditional design flow, where the verification effort represents 70% of the total design time, will yield in more time spent on test-bench development and simulation runs. The result is 192 days as the total development time for this project, compared to 131 days using the improved design flow. This represents a productivity gain of around 32% over a traditional design flow that has limited test-bench components reuse and software interoperability. But the implementation HW/SW reduced the number of clock cycle: 1334722 to 158044 times of execution. The reduction on the total execution time of the JPEG algorithm was 88. 15%.
In this chapter, we presented a new approach based on the integration systemC in matlab / simulink. The capital advantage of this approach is the possibility of modeling and verifying the overall system within the same design environment. The result is shorter design cycles for applications using heterogeneous architectures. The co-simulation interface we presented a method for reducing the time spent on validation and verification while improving overall test-bench quality. MATLAB/Simulink assists the SystemC verification environment in a unified approach. It has been shown that the methodology allows complex stimulus generation and exhaustive data analysis for the design under verification. As FPGA designs encompass larger and larger systems, the need to efficiently model the complex external environment during the architecture and verification phases becomes greater. The whole verification flow has been evaluated, using an example. It has been shown, that the usage of the extended verification flow saves a significant amount of time during the development process. The proposed platform is tested on the JPEG compression algorithm. The execution time of such algorithm is improved by 88.15% due to the hardware implementation of the Matlab mult16 Function using SystemC. As future works, we aim to test our platform with the whole video compression chain using MPEG4 modules and Software-Defined Radio (SDR). It includes hardware and software components that require rigorous verification all along the design flow.
Soybean (Glycine max [L.]) is a leguminous plant that can form a symbiotic relationship with the nitrogen-fixing group of bacteria living in the rhizosphere, which are generally termed as rhizobia. In the Philippines, soybean production has been limited by the poor grain yield which leads to the importation of more than 90% of the country’s demand. Thus, it is essential to look for an alternative way to increase the volume of production per unit area.
The research about tropical bradyrhizobia indicated a high diversity of species and their distribution has been reported to be due to several abiotic and biotic factors such as soil acidity [1, 2, 3], alkalinity [3, 4], temperature [1, 5, 6, 7, 8, 9, 10, 11], climate [12, 13], soil water status [14, 15], soil type [2, 14, 16, 17, 18], and soil management or cultural practices [2, 14, 19, 20, 21, 22]. In case of the Philippines, the pioneer research that was able to identify the most dominant species of bradyrhizobia in the country reported that B. elkanii species was the most abundant, followed by the B. diazoefficiens, B. japonicum, and some yet unclassified Bradyrhizobium sp. [14]. In this later study, it was identified that the distribution of these indigenous species of bradyrhizobia were influenced mainly by the water status of the soil, followed by soil pH, nutrient content, and soil type.
Previous studies have reported that aside from the various agro-environmental factors, the competition with the native rhizobia is a hindrance for a successful inoculation [23, 24]. The utilization of inoculants for legumes had shown promising results for the increase in grain yield as evidenced by recent reports [25, 26]. The role of the biological nitrogen fixation (BNF) in providing the N requirement of the plant in a natural way has been deemed necessary especially these times that the soil has become more degraded due to over-fertilization. The indiscriminate use of NPK fertilizer could cause soil pollution and less crop production [27]. Therefore, it is essential to select and evaluate the symbiotic competitiveness of the indigenous strains which are native and existing in high density in the country. The use of different genetic markers to accurately identify the rhizobia for taxonomic purposes has been proposed [28] and so we have used three genetic markers such as the 16S rRNA gene, 16S-23S rRNA gene internal transcribed spacer (ITS) region, and the rpoB housekeeping gene.
Thus, this study was formulated with the aim to utilize the recently identified indigenous bradyrhizobia in the Philippines and characterize their symbiotic performance with the local soybean cultivars.
The soil samples were collected from 11 locations in the Philippines, where some basic information on the sites are listed in Table 1. The collection of soil was conducted by first removing the surface litters then, obtaining a bar of soil with a dimension of approximately 20 cm in depth and 3 cm in thickness that weighs about 1 kg. A total of 10 subsamples per location were obtained and were mixed thoroughly until a 1 kg of composite soil sample was taken. A 0.5 kg soil was air-dried for the chemical analyses while the remaining 0.5 kg of the fresh soil was used for the soybean cultivation.
Result of the soil chemical analysis on the 11 locations in the Philippines.
Mason et al., 2018
This study
The cultivation of soybean was performed using a 1-L capacity culture pots (n = 3). Each pot was filled with vermiculite and a N-free solution [29] was added at 40% (vol/vol) water content. The culture pots were sterilized by autoclaving for 20 min at 121°C. Meanwhile, the soybean seeds were surface-sterilized by soaking into a 70% EtOh for 30 s, then by a diluted sodium hypochlorite solution (0.25% available chlorine) for 3 min and followed by washing with sterile distilled water for about 6–8 times. Then, a 2–3 g of soil sample was placed on the vermiculite at a depth of about 2–3 cm, the seeds were sown on the soil and the pot was weighed and recorded. The plants were grown inside a growth chamber for 28 days at 28°C (8 h, night) and 33°C (16 h, day) then were supplied weekly with sterile distilled water until the initial weight of the pot was reached.
After 28 days, approximately 20 random nodules were collected from the roots of each soybean plants and were sterilized with 70% EtOh and sodium hypochlorite solution as previously described [29]. Each nodule was homogenized with sterile distilled water in a microtube and streaked on to a yeast-extract mannitol agar (YMA) plate [30]. The YMA plate was incubated in the dark at 28°C for about 1 week until a single colony was formed. After then, the single colony was streaked on to a YMA plate containing a 0.002% (wt/wt) bromothymol blue (BTB) [31] and was incubated as above. Repeated streaking was done until a pure single colony was obtained which was cultured for about 3–4 days in a HEPES-MES (HM) broth culture [32, 33] at 28°C in a shaker for 120 rpm. After then, the bacteria cells were collected by centrifugation at 9000×g and washed with sterile distilled water. The DNA was extracted by using BL buffer as described [34] from the method reported by Hiraishi et al. [35].
For the amplification of the 16S rRNA gene, the primer set: 16S-F: 5′ AGAG TTTGATCCTGGCTCAG-3′ and 16S-R2: 5′- CGGCTACCTTGTTACGACTT-3′ [36]. The PCR tubes were then placed in the PCR Thermal Cycler (TaKaRa Co. Ltd.) with the following conditions: pre-run at 94°C for 5 min; followed by 30 cycles of denaturation at 94°C for 1 min, annealing at 55°C for 1 min, and extension at 72°C for 1 min. Final extension was set at 72°C for 10 min and indefinite preservation at 4°C.
On the other hand, the PCR amplification of the ITS region was conducted using the following primer set: Bra-ITS-F: 5-GACTGGGGTGAAGTCGTAAC-3′ and Bra-ITS-R1: 5′-ACGTCCTTCATCGCC TC-3′ [6]. The PCR cycle for the ITS region was almost the same with the 16S rRNA gene except for a shorter denaturation and annealing periods which were conducted at 30 s for each step.
For the rpoB gene, simplification was done using the following primer sets: rpoB83F: 5′-CCTSATCGAGGTTCAC AGAAGGC-3′ and rpoB1540R: 5′-AGCTGCGAGGAACCGAAG-3′ [37]. The PCR cycle conditions were as follows: pre-run at 94°C for 5 min; followed by 30 cycles of denaturation at 94°C for 30 s, annealing at 60°C for 1 min, and extension at 72°C for 1 min. Final extension was set at 72°C for 5 min and indefinite preservation at 4°C.
The successfully amplified products were subjected to the RFLP treatment using four restriction enzymes which were HhaI, HaeIII, MspI, and XspI. For the rpoB gene, the enzymes that were used for RFLP are HaeIII, MspI, and AluI. The reference strains that were used in this study are the Bradyrhizobium USDA strains (B. japonicum USDA 4, 6T, 38, 62, 115, 122, 123, 124, 125, 127, 129, 135, B. diazoefficiens USDA 110T, B. elkanii 31, 46, 61, 76T, 94, 130, and B. liaoningense 3622T) which were previously described [38]. This was done in a 10-μL reaction mixture containing a 2.5-μL amplified PCR product and was incubated in a 37°C for 16 h. Afterward, a 3–4% agarose gel was used in a submerged gel electrophoresis for about 60 min, stained with ethidium bromide and the patterns were visualized using a Luminiscent Image Analyzer LAS-4000 (FUJIFILM Tokyo, Japan).
After the amplification and the RFLP treatment of the 16S rRNA gene, a single-strain inoculation test was conducted for all the amplified isolates that shared the same restriction enzymes’ fragment patterns with the USDA Bradyrhizobium reference strains. This was done to confirm the strain’s capability to nodulate soybean and was tested on two local varieties which are the PSB-SY2 and Collection 1 which are both commercially available across the country.
The cultivation of soybean was conducted as described above, but without soil. Each isolate was cultured in a YM broth (YMB) [30] at 28°C for about 1 week on a shaker. After then, the cultures were diluted with sterile distilled water at about 106 cells mL−1 and were inoculated on the cultivated soybean at a rate of 1.0 mL per seed. This was done with three replications. After inoculation, the weight of the pot was recorded and it was placed inside a growth chamber with a condition set to mimic the average temperature in the Philippines at 26°C (8 h, night) and 33°C (16 h, day). The same condition was used for the cultivation of an uninoculated control and a positive control pot that was inoculated with B. diazoefficiens USDA110. The pots were kept inside the growth chamber for 28 days and were supplied weekly with sterile distilled water until the initial weight of each pot was reached.
According to the similarities of the band patterns through the RFLP treatment, a representative of the most abundant isolates was chosen for each location. In total, there were 11 isolates that were selected to confirm the nucleotide sequence of the 16S rRNA gene and the ITS region. The sequence primers that were used were reported previously [22]. From the PCR amplified product, the samples were purified according to the protocol of the manufacturer (Nucleospin® Gel and PCR Clean-up; Macherey-Nagel, Germany). Then, the samples were sent to the company for the sequence analysis (Eurofins Genomics, Tokyo, Japan).
Then, the Basic Local Alignment Search Tool (BLAST) program in DNA Databank of Japan (DDBJ) was used to determine the nucleotide homology of the isolates. Only the sequences with a similarity of at least 99% for the 16S rRNA and 96% for the ITS region with our isolates were retrieved from the BLAST database. The alignment was performed using the ClustalW and Neighbor-Joining [21] method was used to construct the phylogenetic trees. The genetic distances were computed using the Kimura 2-parameter model [39] in the Molecular Evolutionary Genetic Analysis (MEGA v7) software [40]. Subsequently, the phylogenetic trees were bootstrapped with 1000 replications. All the nucleotide sequences determined in this study were deposited in DDBJ at
The soil samples that were used in this study were all slightly to moderately acidic (5.22–6.64) with non-saline condition (0.05–0.20 dS/m), low nutrient status as evidenced by low amounts of NPK and CEC (Table 1). These values are generally typical of agricultural soils that are used for crop production all throughout the year. These results showed that the soils used in this study have low fertility status that indicated the need for soil restoration strategies.
The growth morphologies of the pure single colony for each strain of bradyrhizobia were characterized and listed in Table 2. All the isolates were slow growers which were able to form single colonies measuring about 2 mm between 5 and 7 days upon streaking on YMA plates and incubation in a dark room. Based on the morphology, the isolates were grouped into three. Group I include the isolates IS-2, NE1–6, NR-2, and BO-4 which were translucent and the colonies are circular in shape with slightly convex elevation and an entire margin. When they were manipulated with a needle, the colony was liquid. Group II include the isolates BA-24, SO-1, LT-3, and SK-5 were translucent with circular colonies, convex elevation with entire margin. When manipulated with a needle, the colonies have mucoid viscosity. On the other hand, last group (III) are the isolates GI-4 and NE2-37 which have similar growth morphology with Group II except that their viscosity was intermediate between liquid and mucoid. All the isolates produced alkaline substances when grown on YMA plate with BTB which is an indication of the Bradyrhizobium genus.
Characterization of the morphology of the indigenous bradyrhizobia isolated from Philippines’ soil according to their growth on Yeast-Extract Mannitol Agar plate medium [30].
As seen in Figure 1, it is evident that the 11 most abundant indigenous soybean rhizobia in the Philippines are classified under the genus Bradyrhizobium, and are separated into its two species, B. japonicum and B. elkanii, according to the phylogenetic tree from the sequence analysis of the 16S rRNA gene. To further confirm the classification of the indigenous bradyrhizobia, the phylogenetic trees constructed from the ITS region and the rpoB gene are presented in Figures 2 and 3, respectively. For the ITS region and the rpoB gene, the isolates were distinctly grouped into three species, B. elkanii, B. japonicum, and B. diazoefficiens. Additionally, an independent cluster composed of the representative isolates GI-4 and NE2–37 that are seen in the ITS region and rpoB phylogenetic trees were treated as Bradyrhizobium sp. due to their nucleotide divergence with the known species from the BLAST engine.
Phylogenetic tree based on the sequence analysis of the 16S rRNA gene. The tree was constructed using the Neighbor-Joining method with the Kimura 2-parameter (K2P) distance correlation model and 1000 bootstrap replications in MEGA v.7 software. The accession numbers are indicated only for sequences obtained from BLAST. The isolates in this study are indicated with letters and number combinations, for example: BO-4–isolate no. 4 collected from Bohol.
Phylogenetic tree based on the sequence analysis of the 16S-23S rRNA internal transcribed spacer (ITS) region. The tree was constructed using the Neighbor-Joining method with the Kimura 2-parameter (K2P) distance correlation model and 1000 bootstrap replications in MEGA v.7 software. The accession numbers are indicated only for sequences obtained from BLAST. The isolates in this study are indicated with letters and number combinations, for example: BO-4–isolate no. 4 collected from Bohol.
Phylogenetic tree based on the sequence analysis of the rpoB housekeeping gene. The tree was constructed using the Neighbor-Joining method with the Kimura 2-parameter (K2P) distance correlation model and 1000 bootstrap replications in MEGA v.7 software. The accession numbers are indicated only for sequences obtained from BLAST. The isolates in this study are indicated with letters and number combinations, for example: BO-4–isolate no.4 collected from Bohol.
Meanwhile, the distribution of the most abundant soybean bradyrhizobia in the country is shown in Table 3, which was classified according to the results of the sequence analysis of the three genetic markers used in this study. From here, it can be seen that 4 of the 11 locations were dominated with B. elkanii species (37.74%), 3 locations were dominated by the isolates under the B. diazoefficiens (28.54%), whereas 2 locations each were dominated by the species of B. japonicum (16.98% and Bradyrhizobium sp. (16.74%). This indicated that in the Philippines, the species of B. elkanii is the most prevalent in terms of population and the most widespread in terms of location as its presence was detected even in minor populations on all the locations except for one, which was Sorsogon.
Percentage distribution of the dominant Bradyrhizobium species in the Philippines as identified from the sequence analysis of the 16S rRNA gene, 16S-23S internal transcribed spacer (ITS) region, and rpoB housekeeping gene.
Upon classification, it is important to determine the capability of the indigenous bradyrhizobia for their symbiotic performance and N-fixation ability. As can be seen in Figure 4A, although USDA110 strain has the highest N-fixation ability, it should be noted that the amount of N that was fixed by B. elkanii IS-2 is the highest among all the indigenous bradyrhizobia isolated from the Philippines’ soil on Rj4 plants. However, the N-fixation ability of IS-2 was comparably similar with other strains (GI-4, NE2–37, and SK-5) with the non-Rj plants. The lowest N-fixation ability was observed from the strain LT-3 which was classified under the B. diazoefficiens species. This suggested that the process of biological N-fixation is a mutual relationship that is influenced by both the plant and the rhizobia and that the plant-rhizobia compatibility should be taken into consideration for inoculation strategies.
Characterization of the dominant indigenous Bradyrhizobium strains isolated from the 11 locations in the Philippines based on the (A) amount of Nitrogen fixed (B) nodulation ability and (C) symbiotic efficiency as influenced by the single-strain inoculation test against the reference strain B. diazoefficiens USDA110 for the two soybean cultivars from the Philippines. Different letters indicate a significant difference by Tukey’s test at p > 0.05, n=3, bar=SE.
Presented in Figure 4B is the nodulation test performed on the strains and it can be seen for Rj4 plants, there was not much significant difference in the nodulation ability of the strains, except for the low nodulation ability that was observed for the BO-4. In contrast, a significant difference in the nodulation ability was detected on the strains upon inoculation on the non-Rj plants. Although all the strains were able to form nodules on both soybean cultivars, the strains GI-4, NR-2, and SK-5 obtained the highest number of nodules for the non-Rj plants.
On the other hand, the symbiotic efficiency of the strains used in this study is presented in Figure 4C. Similar with the N-fixation ability, the USDA110 still possesses the highest symbiotic efficiency. But among all the indigenous bradyrhizobia, the strain IS-2 obtained the highest efficiency regardless of the Rj genotype of the soybean plants. As with the N-fixation, LT-3 obtained the least efficiency for symbiosis. This result indicated that the symbiotic efficiency of the rhizobia might not be directly influenced by the Rj genotype of the plant.
The distribution of the most dominant and abundant species of soybean bradyrhizobia in the Philippines are reported in this study along with the characterization of their growth morphology. According to our earlier reports, we have elucidated that the Philippines was dominated by the soybean-nodulating bradyrhizobia that were classified under the B. elkanii species and the most important agro-environmental factors that affected their diversity and prevalence in the country was the similarity of soil pH, salinity, and temperature in the study locations [5, 14]. Our observation that there are abundant and high diversity of indigenous bradyrhizobia in the Philippines is similar with previous reports in other sub-tropical and tropical regions [12, 25, 41, 42, 43, 44]. The temperate regions of Japan and USA were studied in the past and were reported to be dominated by species of B. japonicum and B. diazoefficiens [6, 9, 10, 11, 13, 45]. Our report showed that the distribution of bradyrhizobia in a tropical region like the Philippines seemed to be different from those of temperate regions.
Meanwhile, it was included in a recent report that the distribution and abundance of B. diazoefficiens and B. japonicum at specific locations were due to the longer period of flooding conditions [14]. The effect of nutrient content and soil type were also correlated with the abundance of these two species. In a report by Shiina et al. [17], it was stated that the predominance of B. diazoefficiens was observed on more anaerobic condition; whereas, B. japonicum was predominant on aerobic soils which was supported by another study [18]. Additionally, it was reported that B. diazoefficiens becomes predominant with enhanced flooding condition [15]. These results confirmed that our observations for the abundant of B. diazoefficiens, followed by B. japonicum and Bradyrhizobium sp. on flooded areas in the country which were usually used for planting rice.
In this report, the symbiotic performance, N-fixation and nodulation ability of the indigenous soybean bradyrhizobia form the Philippines were evaluated against that of the B. diazoefficiens USDA110 strain. The USDA110 has been extensively used in the world as a model strain for soybean inoculation due to its high ability for N-fixation and symbiotic efficiency [25, 46, 47]. Additionally, its possession of a complete set of denitrification genes that allows the release of N2 back into the atmosphere makes it an ideal strain also for climate change mitigation studies [17, 48, 49, 50].
Therefore, we hypothesized that the indigenous isolates SO-1, LT-3, and SK-5, which were phylogenetically clustered under the USDA110 would also prove to be as effective N-fixer and efficient microsymbiont of soybean cultivars from the Philippines. However, our results indicated that the N-fixation ability and symbiotic efficiency of LT-3 and SO-1 were very low in comparison to the other indigenous isolates. For the low performance of these two isolates, it is hypothesized that the inherent ability of these strains to fix N and establish a symbiotic relationship with soybean is low. This could be explained by the fact that their nodulation ability was comparably similar with the other strains which possess higher N-fixation ability and symbiotic efficiency. In contrast, the isolate IS-2, which was clustered under the B. elkanii species, showed the highest symbiotic efficiency for both Rj-genotypes of the soybean cultivar used and the highest N-fixation ability for Rj4 plants. In a previous report, the Rj genes that could restrict the nodulation of soybean by some strains of bradyrhizobia was summarized [51] but in case of our present report, all the strains in this study were not restricted by the two Rj-plants that were used. This led us to consider that the low N-fixation and symbiotic performance of some strains were not due to the restrictions from the Rj-genotypes of the plants but could be attributed to the strains’ intrinsic capabilities. These observations might explain the reason for low yield of soybean in the Philippines. It was reported that many strains of B. elkanii were relatively inefficient microsymbionts of soybean and can induce chlorosis in soybean plants [52]. In a previous report [53], the high temperatures in tropical regions can limit the nodulation which could explain the low soybean yield.
It was expected that the strains which were classified as B. diazoefficiens could provide a better symbiotic performance than the other strains that were collected. However, the data showed that B. elkanii might establish a better symbiosis with local soybean cultivars in the Philippines. This result is crucial in order to devise strategies on how to increase the local production of soybean by inoculation with the indigenous strains.
Upon considering these results with the N-fixation and symbiotic performance ability of the strains, the number of nodules that can be formed from the single-strain inoculation does not seem to influence the amount of N that each strain can fix nor their symbiotic ability.
In this report, we have revealed that the distribution of tropical soybean bradyrhizobia seemed to be different than those of temperate bradyrhizobia in terms of population dominance of B. elkanii on higher temperature region like the Philippines. Additionally, it is proposed that for the Philippines, the most efficient N-fixer and symbiotically efficient species of bradyrhizobia would be B. elkanii. Yet, our results were made under the laboratory conditions only, so the results that were obtained here might not be as expected when done in field condition. For future research, utilization of more local soybean varieties with different soil types both in a controlled environment and on natural field condition would be beneficial to target the development of a site-specific and useful potential soybean inoculant. The data generated in this report would be beneficial for the augmentation of inoculation strategies in the country.
The authors would like to acknowledge the contributions of John Philip Tanay, Emmanuel Victor Buniao, Mary Joy Portin, and Maria Leah Sevilla of Central Luzon State University for their help on some laboratory experiments. This work was supported by the JSPS Grant-in-Aid for Scientific Research (KAKENHI Grant Number: 18K05376).
The authors declare no conflict of interest.
IntechOpen implements a robust policy to minimize and deal with instances of fraud or misconduct. As part of our general commitment to transparency and openness, and in order to maintain high scientific standards, we have a well-defined editorial policy regarding Retractions and Corrections.
",metaTitle:"Retraction and Correction Policy",metaDescription:"Retraction and Correction Policy",metaKeywords:null,canonicalURL:"/page/retraction-and-correction-policy",contentRaw:'[{"type":"htmlEditorComponent","content":"IntechOpen’s Retraction and Correction Policy has been developed in accordance with the Committee on Publication Ethics (COPE) publication guidelines relating to scientific misconduct and research ethics:
\\n\\n1. RETRACTIONS
\\n\\nA Retraction of a Chapter will be issued by the Academic Editor, either following an Author’s request to do so or when there is a 3rd party report of scientific misconduct. Upon receipt of a report by a 3rd party, the Academic Editor will investigate any allegations of scientific misconduct, working in cooperation with the Author(s) and their institution(s).
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\\n\\nA Statement of Concern detailing alleged misconduct will be issued by the Academic Editor or publisher following a 3rd party report of scientific misconduct when:
\\n\\nIntechOpen believes that the number of occasions on which a Statement of Concern is issued will be very few in number. In all cases when such a decision has been taken by the Academic Editor the decision will be reviewed by another editor to whom the author can make representations.
\\n\\n3. CORRECTIONS
\\n\\nA Correction will be issued by the Academic Editor when:
\\n\\n3.1. ERRATUM
\\n\\nAn Erratum will be issued by the Academic Editor when it is determined that a mistake in a Chapter originates from the production process handled by the publisher.
\\n\\nA published Erratum will adhere to the Retraction Notice publishing guidelines outlined above.
\\n\\n3.2. CORRIGENDUM
\\n\\nA Corrigendum will be issued by the Academic Editor when it is determined that a mistake in a Chapter is a result of an Author’s miscalculation or oversight. A published Corrigendum will adhere to the Retraction Notice publishing guidelines outlined above.
\\n\\n4. FINAL REMARKS
\\n\\nIntechOpen wishes to emphasize that the final decision on whether a Retraction, Statement of Concern, or a Correction will be issued rests with the Academic Editor. The publisher is obliged to act upon any reports of scientific misconduct in its publications and to make a reasonable effort to facilitate any subsequent investigation of such claims.
\\n\\nIn the case of Retraction or removal of the Work, the publisher will be under no obligation to refund the APC.
\\n\\nThe general principles set out above apply to Retractions and Corrections issued in all IntechOpen publications.
\\n\\nAny suggestions or comments on this Policy are welcome and may be sent to permissions@intechopen.com.
\\n\\nPolicy last updated: 2017-09-11
\\n"}]'},components:[{type:"htmlEditorComponent",content:'IntechOpen’s Retraction and Correction Policy has been developed in accordance with the Committee on Publication Ethics (COPE) publication guidelines relating to scientific misconduct and research ethics:
\n\n1. RETRACTIONS
\n\nA Retraction of a Chapter will be issued by the Academic Editor, either following an Author’s request to do so or when there is a 3rd party report of scientific misconduct. Upon receipt of a report by a 3rd party, the Academic Editor will investigate any allegations of scientific misconduct, working in cooperation with the Author(s) and their institution(s).
\n\nA formal Retraction will be issued when there is clear and conclusive evidence of any of the following:
\n\nPublishing of a Retraction Notice will adhere to the following guidelines:
\n\n1.2. REMOVALS AND CANCELLATIONS
\n\n2. STATEMENTS OF CONCERN
\n\nA Statement of Concern detailing alleged misconduct will be issued by the Academic Editor or publisher following a 3rd party report of scientific misconduct when:
\n\nIntechOpen believes that the number of occasions on which a Statement of Concern is issued will be very few in number. In all cases when such a decision has been taken by the Academic Editor the decision will be reviewed by another editor to whom the author can make representations.
\n\n3. CORRECTIONS
\n\nA Correction will be issued by the Academic Editor when:
\n\n3.1. ERRATUM
\n\nAn Erratum will be issued by the Academic Editor when it is determined that a mistake in a Chapter originates from the production process handled by the publisher.
\n\nA published Erratum will adhere to the Retraction Notice publishing guidelines outlined above.
\n\n3.2. CORRIGENDUM
\n\nA Corrigendum will be issued by the Academic Editor when it is determined that a mistake in a Chapter is a result of an Author’s miscalculation or oversight. A published Corrigendum will adhere to the Retraction Notice publishing guidelines outlined above.
\n\n4. FINAL REMARKS
\n\nIntechOpen wishes to emphasize that the final decision on whether a Retraction, Statement of Concern, or a Correction will be issued rests with the Academic Editor. The publisher is obliged to act upon any reports of scientific misconduct in its publications and to make a reasonable effort to facilitate any subsequent investigation of such claims.
\n\nIn the case of Retraction or removal of the Work, the publisher will be under no obligation to refund the APC.
\n\nThe general principles set out above apply to Retractions and Corrections issued in all IntechOpen publications.
\n\nAny suggestions or comments on this Policy are welcome and may be sent to permissions@intechopen.com.
\n\nPolicy last updated: 2017-09-11
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Today his focus is on defining the growth and development strategy for the company.",institutionString:null,institution:{name:"TU Wien",country:{name:"Austria"}}},{id:"19816",title:"Prof.",name:"Alexander",middleName:null,surname:"Kokorin",slug:"alexander-kokorin",fullName:"Alexander Kokorin",position:null,profilePictureURL:"https://mts.intechopen.com/storage/users/19816/images/1607_n.jpg",biography:"Alexander I. Kokorin: born: 1947, Moscow; DSc., PhD; Principal Research Fellow (Research Professor) of Department of Kinetics and Catalysis, N. Semenov Institute of Chemical Physics, Russian Academy of Sciences, Moscow.\r\nArea of research interests: physical chemistry of complex-organized molecular and nanosized systems, including polymer-metal complexes; the surface of doped oxide semiconductors. 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