A novel portable underwater acoustic modem is proposed in this paper for covert communication between divers or underwater unmanned vehicles (UUVs) and divers at a short distance. For the first time, real dolphin calls are used in the modem to realize biologically inspired Covert Underwater Acoustic Communication (CUAC). A variety of dolphin whistles and clicks stored in an SD card inside the modem helps to realize different biomimetic CUAC algorithms based on the specified covert scenario. In this paper, the information is conveyed during the time interval between dolphin clicks. TMS320C6748 and TLV320AIC3106 are the core processors used in our unique modem for fast digital processing and interconnection with other terminals or sensors. Simulation results show that the bit error rate (BER) of the CUAC algorithm is less than 10 With the growing demand for marine development, underwater acoustic communication (UAC) and networks have been used in many fields, such as marine environmental monitoring, natural disaster warning, etc ,2. FurthBased on the different modulation methods, the modems are divided into several categories including quadrature phase shift keying (QPSK) modems, frequency shift keying (FSK) modems, quadrature amplitude modulation (QAM) modems, and so on. A compact and low power micro-modem  designedCompared to QPSK modulation, FSK modulation is more widely used in modems. A low-power acoustic modem for dense underwater sensor networks using FSK modulation was developed by the University of Southern California in 2006  and was Communication between divers and their commander needs to be kept highly secure and the location of activity has to be kept secret. Using simple UAC, transmitted messages are more vulnerable to being intercepted by the enemy and the location can be easily traced. This calls for covert underwater acoustic communication which keeps the communication between divers highly secure and undetected by eavesdroppers. Some papers ,19,20 haThe primary purpose of this article is to design a Portable Biomimetics-based Covert (PBC) UAC micro-modem and realize covert communication by using real dolphin sounds. The communication carrier waveform in the PBC micro-modem is natural dolphin or whale sounds. In the specific communication process, the dolphin signal will be selected according to the actual situation to realize the effect of covert communication. For example, local dolphin calls should be selected for communication in different sea areas, and the seasonal dolphin calls should be used for communication in different seasons. In order to improve the communication speed and restrain the multipath interference between adjacent symbols, low correlation dolphin calls should be selected. The dolphin- and whale-call samples used in the communication algorithm are stored in the SD card in advance. In the PBC micro-modem, we implemented a variety of bionic communication algorithms as described in ,21,22 acThe remainder of this paper is organized as follows: A comparison of developed devices, commercial devices and the PBC modem is described in With the evolution of technology and the demand for diversification, more and more requirements have emerged in Underwater Wireless Sensor Networks (UWSN). Nam, H. described an energy-aware acoustic modem and tested its performance in underwater experiments in . An omnismission . Due to smission  started smission ,28.A few companies are actively researching UAC modems and have developed many commercial modems. The Atm series modem  made by Based on the comparative analysis of an underwater acoustic modem collated by Sendra, S. and Lloret, J. in ,33, we hAs we can see from Additionally, the PBC modem focuses on the application of CUAC among UWSN nodes, divers or UUVs by using real dolphin or whale sounds and mimicking the sounds of sea creatures which is different from existing modems.The dolphin and whale call samples used in the communication algorithm are stored in the SD card in advance which makes the selection of communication signals more flexible. For example, in the specific communication process, sound signals will be selected according to the actual situation in order to realize covert communication. Local dolphin calls should be selected for communication in different sea areas, and seasonal dolphin calls should be used for communication in different seasons.These unique features make our PBC modem significantly different from existing developed and commercial modems.Our modem is designed specifically for divers to communicate with their partners or UUVs securely as shown in The conventional modem structure block diagram is illustrated in In our design, the analog and digital circuits are put together to reduce the volume of the hardware. It transmits the instructions via UART and acquires the audio signal by using the CODEC and Enhanced Direct Memory Access (EDMA) modules. We use Inter-Integrated Circuit (IIC) bus to control the TLV320AIC3106 . The desThe core signal processor in our design is TMS320C6748 . It is aThe analog to digital converter (ADC) and digital to analog convertor (DAC) for the modem is TLV320AIC3106. It is a low-power stereo audio codec with a stereo headphone amplifier, as well as multiple inputs and outputs programmable in single-ended or fully differential configurations. The sampling rate of the stereo audio ADC and DAC can vary between 8 kHz and 96 kHz. Extensive register-based power control is included, enabling stereo 48 kHz DAC playback as low as 15 mW from a 3.3 V analog supply, making it ideal for the portable battery powered UAC modem. The TLV320AIC3106 contains integrated microphone bias, a digitally controlled stereo microphone preamplifier, and automatic gain control (AGC), with mix/mux capability among the multiple analog inputs making the input SNR and the output SNR reach 102 dB and 92 dB, respectively.In this design, AIC3106 communicates with DSP through the McASP and IIC interface. DSP sends a control signal to AIC3106 through the IIC interface. The data received or sent by AIC3106 is transmitted through the McASP serial interface to DSP.The analog circuit receives the signal from the digital circuit at which point the digital signal is changed into analog signal through AIC3106. After being amplified by the power amplifier, the signal is transmitted by the transducer as shown in the following At the reception, first the acoustic signal is transformed into a weak electronic signal by the transducer, then the preamplifier of the analog circuit will amplify the signal. Finally, the amplified results are transmitted to the digital circuit where they wait for CODEC perform the next operation. The process is shown in Piezoelectric transducer excitation has been previously carried out mainly using three power amplifier types: Class-B; class-D; and class-AB. When the class-B power amplifier becomes functional, positive and negative channel transistors usually remain in a closed state unless there is a signal input, which can be elaborated as when the positive phase signal is received, only the positive phase channel starts working while the negative phase channel remains closed. Furthermore, the two channels will not work simultaneously to avoid any power loss in the part where there is no signal. The use of a commercial class-AB amplifier can avoid the drawbacks of the class-B amplifier. Exploring the actual need and selecting the best available power amplifier, we decided to use the class-AB power amplifier in this design. The TDA2030A is a monolithic IC, intended for use as a low-frequency class-AB amplifier. With VS max = 44 V, it is particularly suitable for more reliable applications without regulated supply and for 35 W driver circuits using low-cost complementary pairs. The TDA2030A provides high output current and has very low harmonic and cross-over distortion. Furthermore, the device incorporates a short circuit protection system comprising an arrangement for automatically limiting the dissipated power so as to keep the working point of the output transistors within their safe operating area. A conventional thermal shut-down system is also included.Normally, a class-D power amplifier is more efficient than a class-AB power amplifier. However, the class-AB amplifier peripheral circuit is relatively simple, which is more conducive to the miniaturization of the modem. In addition, the output audio quality of the class-AB power amplifier is better and less noisy than that of the class-D amplifier. With the requirement of modem miniaturization, it is difficult for class-D power amplifiers to achieve both low interference and circuit scale miniaturization at the same time and it may produce high-frequency harmonics. In general, the duration of underwater diving activity is several hours. Even though class-AB power amplifiers are less efficient than class-D power amplifiers, they can still meet this demand.The transducer converts an acoustic wave signal to a differential voltage signal; however, the voltage signal is quite weak. For long distance transmissions, it is only a few tens of micro volts. However, in some cases, voltage can reach tens of millivolts, which exceeds the preamplifier requirements. At the same time, the programmable gain is very important for the realization of the actual project. The OPA348 series amplifiers are single supply, low-power, CMOS op-amps in micro packaging. Featuring an extended bandwidth of 1 MHz, and a supply current of 45 A low supply current of 45 Instead of a simple pre-amplifier, the analog reception amplifier in this modem includes band pass filtering and an adjustable gain amplification. As the application’s environment demands a wideband filter, we use an analog amplifier to build a band pass filter by using a Butterworth low-pass filter and a second-order Butterworth high-pass filter, whose range is adjustable. The reason for choosing it is the flexibility to control the cut off frequency.The amplifier programmable control amplification is less than 40 dB if the frequency of the received signal is above 1 kHz. The signal could be amplified the second time in the AIC3106.The hardware design of the underwater acoustic modem is shown in The main purpose of this design is to communicate covertly between divers or divers and UUVs. When the divers are closer to the target and the instructions are still on the way, the divers are more vulnerable to being detected if the target has diver detection sonar. The application of bionic communication will make the enemy misjudge the diver’s action as the communication signal will be excluded as it sounds like cetacean calls.We modulate the signal based on the time interval to overcome the sound exposure derived from traditional fixed carrier modulation, treating the communication signal as ocean biological noise to achieve covert communication.In this section, the main content is divided into two parts, the first part is the algorithm simulation and realization while the second part is the software design and algorithm implementation process.This section introduces the specific process of algorithm implementation while referring to the literature  which isIn the modulation process, the data from the serial port is encoded first and each six bits are converted to decimal digits. The length of the time delay is calculated according to the time delay resolution. Delay difference is modulated between the interval of two signals according to the calculation. After assembling all click signals and time delay together, the synchronization head and the protection interval are added to the header of the signal. The process flow chart of bio-signal modulation is shown in i = 1,2,3,⋯,L) is the is the coding time, which refers to the time delay difference between two click signals. Each click signal time duration is represented by j = 0,1,2,⋯,L). For each n bits of encoded information, the encoding time is divided into  curve of the algorithm under white Gaussian noise by simulation. At the same time, we used the real lake channel to test the performance of the algorithm, and used the matching pursuit (MP)  algorithThe underwater channel is derived from Songhua Lake in China. The water depth was about 40 m. The transmitter was about 13 m and the receiving hydrophone was about 12 m below the boats with a distance of 820 m. The simulation results show that the BER is less than 10The software flowchart of this modem is shown in The initialization of the system will be carried out after powering up the modem, including system PSC, interrupt, EDMA, IIC, AIC3106, serial port initialization, etc. In addition to the initialization of these modules, a few more steps are needed to complete the algorithm implementation.To realize the algorithm on DSP, we take the whale clicks converted to sixteen bits of vector data. The data is stored in the SD card in the modem to realize the modulation and demodulation process in advance. In the initialization process, there are two serial communication processes between the Modem and host computer; the first one is to determine the selection of dolphin calls from the SD card and the second command is to determine the modem working in sending or receiving mode.If it is in receiving mode, we will carry out the FFT process on the frame synchronization signal—it is mainly used in the fast correlation operation to find the synchronization signal and reduce the computing time. After completing all of the above steps, the system is initialized.After the initialization, the whole system is working in a standby state, awaiting the transmission of serial instructions. If the system receives the sending instructions, it will continue to receive the data from the serial port and begin to carry out the algorithm modulation after receiving the cut-off character instruction.If the system receives the instructions of data acquisition from the serial port, it begins to collect the signal and carries on the fast correlation operation. After finding the signal by seeking the correlation peak, the system demodulates the signal and the results are sent through the serial port to the host computer.To verify the functionality and performance of the PBC micro-modem, indoor experiments were conducted in a channel pool as shown in According to the frequency of the click signal, we use the 2–8 kHz transducer and BRUEL &KJAER’s 8105 hydrophone to receive the signal. As the demodulation is mainly carried out by signal correlation, in order to reduce the bit error rate, we take the channel and noise effects into account. We removed the signal from the call library if the correlation coefficient between them is more than 0.30, retaining only the number c1, c2, c3, c4, c6 signals.To evaluate the similarity between the dolphin-call samples and the received signals through the pool channel, we collected the received signals from the receiver, and the signal and call samples were compared in the spectrogram as follows. A comparison of the spectrogram of the call samples and the received signals is shown in The time–frequency analysis and demodulation results are shown in The purpose of this experiment is to verify the algorithm and the performance of the modem. According to the specific needs, we can increase the distance between the clicks and the number of click signals.In this paper, we have designed a portable micro-modem based on the bionic covert UAC algorithm for underwater sensor networks. Specifically, it is the first time that a modem has been used to communicate using real dolphin-call signals. It opens the door for secure and covert communication—the message between the divers or UUVs and control center cannot be identified. Additionally, the compact design of the modem has many advantages such as being portable for divers, it can be placed on UUV and it can also be used as a standalone unit for a particular application. In particular, it is suitable for combat divers’ information transmission at short distances and other military applications with covert operations. In the pool experiment, we tested the covert UAC algorithm by using the time delay between dolphin sounds and verified that the modem could efficiently perform reliable data transmission over short distances. At a distance of 10 m, a data rate of 27.1 bits per second is achieved. However, work is still in progress and our current work only uses transducers for lab communication. We plan to test our modem in the sea or a lake shortly. We will try to increase the communication distance as well as the data rate. We will also enhance the circuit of the modem, improve its stability, and reduce its output noise. The existing dolphin sounds library can be expanded, and more algorithms need to be developed to imitate dolphin sounds and realize covert communication.


As one of the most important applications in peer-to-peer (P2P) networks, the video-on-demand (VoD) system freely supports video cassette recorder (VCR) operation for users. However, the users may experience significant playback delay after frequent VCR operations in the VoD system, which will affect the quality of experience (QoE) of the users. Hence, selecting an appropriate data-prefetching strategy to support better VCR operation is an important approach to improve the QoE. This paper proposes a data-prefetching strategy (DSA) to determine the most suitable anchor interval by considering the playback delay and positioning satisfaction. According to the DSA, we use the multiple-attribute decision-making (MADM) theory to model the selection of intervals of prefetching data blocks  and the technique for ordering preference by similarity to an ideal solution (TOPSIS) algorithm to solve the MADM. The simulation results show that the DSA strategy obtains higher positioning satisfaction than the existing schemes, which is approximately 60% higher than the anchor points, popular parts of video, and user interests (API)-based method. Moreover, with the increase in network bandwidth, the DSA strategy can minimize the playback delay after VCR operation using relative few extra bandwidths. In recent years, with the rapid development of internet and multimedia technology, increasingly more users have gained access to high-speed internet, and the service of online video-on-demand (VoD)  has beenCompared with the live video system, a significant feature of the VoD system is that it can support the users to perform video cassette recorder (VCR) operations   theory . Based oThe remainder of the paper is structured as follows. The model of the P2P-based VoD system is described in Before stating the research of the data-prefetching strategy, it is necessary to introduce the P2P-based VoD system. This system is an overlay network  built beAs illustrated in When a CN goes online, it must first register with the TS. After the registration is successful, the servable video list of this region is sent to this CN by the TS. The users can select the video that interests them from the video list. After receiving the user’s selection, the CN must determine the download order of the video segments according to the segment selection algorithm. Then, the CN requests the servable peers from the TS and sorts the servable nodes. After selecting the most suitable node as the content provider, the CN can download video segments in order. It is notably important to improve the user’s viewing experience by determining a suitable order to download the video segments, which we will introduce in detail in the following chapters.The segment-downloading sequence affects the viewing experience of the user in the P2P-based VoD system. Therefore, many segment selection strategies were proposed. To support the particularity of the VCR operation in the P2P-based VoD system, data-prefetching strategies were introduced as a specific segment selection strategy, i.e., downloading the data before the current playing point in advance, which is designed to reduce the playback delay after VCR operations. The most mature data-prefetching strategy is the anchor point strategy . When thFirst, we discuss the anchor duration. Each anchor must be a block that can be independently played. Based on the content fragmentation strategy in the P2P-based VoD system in Second, to study the anchor interval, we must consider two factors: playback delay and positioning satisfaction.The playback delay is the time the CN takes to resume playing the video after a VCR operation, as illustrated in When the anchor duration is fixed, if the anchor interval increases, the anchors that are perfected with identical residual download bandwidths will have a wider distribution in the video. When the user randomly jumps to a certain point using a VCR operation, the probability that the anchor near the point that has been downloaded increases, and the probability that the user experiences a delay decreases. Therefore, the average playback delay decreases.We simulated the VCR behavior of a VoD system. The fast-forward and -backward operations compose a notably small percentage (approximately 1%) of the user’s actual operations. As mentioned in ,16, mostThe length of each jump in the VCR operation complies with Weibull distribution , and theAfter the video was played for 1 min, the user randomly performed 20 VCR operations; then, the average playback delay was recorded. As shown in When the user performs a VCR operation, he/she hopes that the player resumes playing the video exactly from the designated point. As mentioned in the anchor-prefetching strategy, the actual playback point of the player does not exactly coincide with the designated point by the user. Thus, the concept of positioning satisfaction is generated.As shown in Satisfaction is a fuzzy concept of people psychology, so we use the membership function of fuzzy mathematics to define the positioning satisfaction. We define that the positioning satisfaction is 1 if the time gap of the actual playback point and the designated point is less than 5 s, and a greater difference implies lower positioning satisfaction. The positioning satisfaction with time gap is calculated according to Equation (2):We have studied how the anchor interval affects the positioning satisfaction using simulations. Since the user more likely jumps forward for a VCR operation ,19. We mIt is not acceptable for the user to experience a long playback delay when they perform a VCR operation, i.e., a shorter playback delay corresponds to a better user experience. According to the analysis in The positioning satisfaction reflects the difference between the actual playback point and the designated point. A smaller difference indicates higher satisfaction of the user. According to the analysis in Therefore, the playback delay and positioning satisfaction are two conflicting factors.As analyzed, the playback delay is a cost factor, and the positioning satisfaction is a benefit factor. Based on the two types of factors, we present the anchor optimization selection strategy DSA. This paper aims at selecting the most suitable scheme from the limited number of optional anchor interval schemes. Hence, it is a typical MADM problem.S+) and negative ideal solution (S−). The basic principle of TOPSIS is using the distance from each candidate to S+ and S− as the criterion to rank the candidates. According to the ranking, we can select the most suitable candidate. The detailed steps of the TOPSIS method are summarized as follows:As one of the most widely used method to solve the MADM problem, the TOPSIS method  proposesStep 1. Construct the normalized decision matrix AFirst, it is important to construct the original decision matrix before the normalization, and the decision matrix V with m candidates and n factors is shown in Equation (3):j-th factor value of the i-th scheme. To eliminate the difference of these two factors, the decision matrix must be normalized. For the benefit factor and cost factor, the normalization method is shown in Equations (4) and (5), respectively.In this paper, the decision matrix V consists of 20 optional schemes and 2 factors.Then, the normalized decision matrix A is obtained:Step 2. Calculate the weight of each factorThe entropy weight is calculated as follows:j:In Equation (7), In Equation (8), Step 3. Construct the evaluation matrix based on the entropy weight:Step 4. Determine the ideal and negative ideal schemesS+ and negative ideal scheme This step determines the ideal scheme Step 5. Calculate the distance of each scheme from the ideal and negative ideal schemesStep 6. Calculate the distance of each scheme from the ideal and negative ideal schemesStep 7. Sort the candidate schemes according to.In this study, we propose 20 optional anchor interval schemes, and the length of the interval is 0.5–10 min with uniform increments. The TOPSIS method is used to comprehensively evaluate the 20 schemes, and the priority order of the candidate schemes is shown in In the TOPSIS method, each factor value of the ideal solution is the optimal value of all candidates. In other words, the ideal solution has the smallest playback delay and highest positioning satisfaction among all candidate schemes. Therefore, the ideal solution can achieve the best viewing experience. Each factor value of the negative ideal solution is the worst value of all candidates. The negative ideal solution will ideally result in the worst viewing experience. In fact, the ideal solution and negative ideal solution do not exist in the proposed candidates. The best candidate has the farthest distance from the negative ideal solution and the shortest distance from the ideal solution. Therefore, the best candidate has the highest viewing experience among all candidates.To verify the rationality of the proposed strategy in this paper, we compared it with the most mature anchor strategy, whose anchor interval is 5 min , and theWe implemented the P2P-based VoD system and data-prefetching algorithm using Java. In the comparative experiment, we simulated the VCR operation process when the user watches a video in a P2P-based VoD system, and the test video bit rate is 600 kbps. After the video was played for 1 min, the user randomly performed 5 times VCR operations every 15 s.In a P2P-based VoD system, the data-prefetching strategy is proposed to minimize the latency that the user must wait after the VCR operation. Therefore, the playback delay is one of the most important indicators to evaluate the validity of a data-prefetching strategy. For identical network bandwidths, a smaller delay indicates a better data-prefetching strategy.As shown in The VoD system enables the users to perform VCR operations and quickly search for interesting content. The users hope that the player resumes playing the video exactly from their designated point after the VCR operation. Positioning satisfaction is the indicator to evaluate the proximity of the designated point and the actual playback point.As shown in The peers in the P2P-based VoD system require auxiliary information to prefetch data, and the bandwidth consumed by the auxiliary information is the extra bandwidth. To prefetch data for the peers using the anchor-prefetching strategy or the DSA strategy, two extra fields must be added to the index file: the anchor length and the list of starting segment numbers for each anchor. When a peer begins watching an on-demand video, the index file from the server or peers must first be obtained and locally saved. Then, the peer requests the segments according to the index file and the user’s playing request. Therefore, to implement these prefetching strategies, one peer must only transmit two additional fields.However, the API strategy prefetches both anchors and popular segments. To achieve this prefetching strategy, adding the two fields of the anchor length and starting segment number for each anchor to the index file is not sufficient, as previously mentioned. To acquire the popular segments of the current system, the server must perceive which segment of the video is currently played by each online peer. To satisfy this requirement, two information fields (the video ID and currently played video segment) should be added to the heartbeat packet, which is periodically sent by peers. The heartbeat packet is a collection of real-time basic information of the peers that must be periodically uploaded to the tracker server (TS) by online peers. The server manages the peers through the heartbeat packet information. A peer sends a heartbeat packet every 30 s by default.When an online peer watches a 60 min video, we assume that the user watches the video for a total of 30 min over a series of VCR operations. The extra bandwidth required for the three strategies is shown in In the API strategy, the peer’s playing information must be added to the periodically sent heartbeat packet, which consumes 20–30 times more bandwidth than the other two strategies. However, the anchor-prefetching strategy and proposed DSA strategy in this paper consume notably little extra bandwidth for each video, which is within the acceptable range.When tens of thousands of online peers watch thousands of on-demand videos in the P2P-based VoD system, the extra bandwidth consumed by the API sharply increases compared to the other two strategies. In other words, the implementation of the API causes a significant system burden. Therefore, the API has poor practicality.In this paper, the optimal data-prefetching scheme is derived using the TOPSIS algorithm based on the MADM theory: the DSA strategy. In order to determine the most suitable data prefetching strategy, we considered factors of different type which can influence user’s viewing experience, such as playback delay and positioning satisfaction. The experiment demonstrates that the proposed DSA strategy in this paper improves the positioning satisfaction by approximately 60% relative to the API strategy. Moreover, the DSA strategy can ensure that the delay performance is relatively good. In addition, the delay performance increases the fastest with the increase in network bandwidth, compared with the other two strategies, and achieving this strategy requires less extra bandwidth. Therefore, the proposed DSA strategy in this paper has the best performance based on the comprehensive evaluation in these three strategies, and it can enable users to obtain a better viewing experience. Also, this paper has presented a model to determine the most suitable prefetching data strategy based on different factors. The model has good extensibility, and can be extended from two factors to multiple factors. This model can also be applied to the segment selection algorithm to determine the downloading order of different types of segments.Due to the limited conditions, the experiments were evaluated by simulations with Java. Hence, some future work is still needed. The performance of the DSA strategy needs to be validated in real experimental environments.


AbstractParatettix sp. was misidentified as Tetrixbolivari. This case highlights the need for correct species identification and provides an opportunity to recommend some aspects of Good Taxonomic Practice (GTP) in Tetrigidae to reduce the number of erroneous identifications.In a recently published paper on colour polymorphism in a Pygmy grasshopper from China  an unide Orthoptera, the members of the family Tetrigidae have a quite complicated taxonomic history, including long list of synonyms and large collections of unidentified specimens. In Europe, it took almost 200 years, from Linnean time to the publication of the European handbook by Tetrigidae taxonomy, researchers from China are currently particularly active, having described 795 species . While the molecular data by Tetrixbolivari, which is unlikely to occur in China and recommend some aspects of Good Taxonomic Practice (GTP) in Tetrigidae.In a recent publication in ZooKeys, Paratettix Bolívar, 1887. This is evident from the traits visible (see for example Tetrigidae). (1) The Median Carina (CM) of the pronotum terminates before reaching the distal pronotal end, (2) the interocular distance is as broad as the eye-span, (3) the fastigium does not protrude in front of the eyes and (4) the long antennae segments slightly broaden towards their terminal end. The first character is very distinctive and the single-most important character aligning the specimens to the genus Paratettix, as outlined in the detailed keys for Europe . A neighbour-joining tree was produced running the software MUSCLE (www.ebi.ac.uk/Tools/msa/muscle/). The resulting tree  and Paratettixpullus Bolívar, 1887, rather than to group with selected members of the genus Tetrix Latreille, [1802]. It should be noted that the gene COI contains a reasonable phylogenetic signal for a smaller number of species of moderate separation time, and was shown to be quite useful for Barcoding purposes in Orthoptera as well (A second line of evidence comes from genetic data. The authors sequenced the gene COI (which is commonly used as Barcoding gene) to examine a proposed correlation between colour morphs and haplotypes. As sequences of COI are available for a wide range of taxa, we deployed a quick analysis of the mitochondrial COI data from the Barcoding of life database , they cluster with the widespread PageBreakEast-Asian species Tetrixjaponica . In summary, both testable records of Tetrixbolivari from China appear to belong to other species.We can add a biogeographic argument, why we question the occurrence of ological  and faunn Europe , the Midn Europe  to Centrn Europe  and Tadzn Europe . The troom China  to our oGTP) to reduce the taxonomic instability in Tetrigidae:We summarize some recommendations for a Good Taxonomic Practice  along with verified molecular data are available, showing photographs of the studied specimens is a helpful practice. It was of great benefit that the article by PageBreak


A mesh resolution of about 0.25 Å (cubic grid space)/0.36 Å (tetrahedron edge length) is found to be most accurate in linear finite element calculation of the PB solvation energy. Computational studies are performed on a few exemplary molecules. The results indicate that all factors, the membrane thickness, the length of periodic box, membrane dielectric constant, pore region dielectric constant, and ionic strength, have individually considerable influence on the solvation energy of a channel protein. This demonstrates the necessity to treat all of those effects in the PB model for membrane protein simulations.Membrane channel proteins control the diffusion of ions across biological membranes. They are closely related to the processes of various organizational mechanisms, such as: cardiac impulse, muscle contraction and hormone secretion. Introducing a membrane region into implicit solvation models extends the ability of the Poisson–Boltzmann (PB) equation to handle membrane proteins. The use of lateral periodic boundary conditions can properly simulate the discrete distribution of membrane proteins on the membrane plane and avoid boundary effects, which are caused by the finite box size in the traditional PB calculations. In this work, we: (1) develop a first finite element solver (FEPB) to solve the PB equation with a two-dimensional periodicity for membrane channel proteins, with different numerical treatments of the singular charges distributions in the channel protein; (2) add the membrane as a dielectric slab in the PB model, and use an improved mesh construction method to automatically identify the membrane channel/pore region even with a tilt angle relative to the  The Poisson–Boltzmann (PB) equation is one of the most popular implicit models to describe the solvent effect through the Boltzmann distribution ,10,11,12The analytic solutions of the PB equation are only available for cases where the computational domain of the biomolecule can be approximated by a simple shape, such as spheres and cylinders. However, in reality the shape of a biomolecule is complex and irregular. Under such circumstances, the PB equation needs to be solved numerically. Essentially, there are three main numerical techniques based on the discretization of the domain of interest into small regions: the finite difference method (FDM), the boundary element method (BEM), and the finite element method (FEM). In this paper, we employ FEM, which is based on a weak variational formulation. The unknown is approximated by a superposition of a set of basis functions ,18,19,20To study membrane proteins, the membrane needs to be implemented in the PB equation framework to account for the sensitivity of the structure and how it functions in its surrounding environment. Consideration of the membrane increases the model complexity. Firstly, the position of the membrane makes the discrete grid/mesh construction more challenging, especially for membrane channel proteins. Secondly, the discrete distribution of membrane proteins on the membrane plane require more specific requirements with the boundary conditions. Effort has been made to include a membrane region in both Generalized Born methodologies ,22,23,24z with the values of z-axis.The simple slab-like membrane setup is commonly used in implicit membrane solvation models. Membrane channel proteins control the diffusion of ions across biological membranes. Therefore, channels are usually end-to-end through and filled with water. on above . In thisIntroducing the membrane region into the implicit solvation model extends the capacity of the PB equation to handle membrane proteins. Usually, there are multiple proteins scattered on the membrane, therefore, a lateral periodic boundary condition can used as a good approximation to simulating the real membrane environment. The use of this type of boundary conditions can avoid boundary effects caused by the finite box size in the traditional PB calculations by using a fixed boundary potential value. In FDM, the lateral periodic boundary condition is accomplished by treating the nodes on one face of the computation grid as if they were adjacent to corresponding nodes from the opposing grid face . In FEM,The solvation energy describing the interaction between the solute and the environment can be roughly decomposed into two parts: electrostatic and non-polar solvation energies. The electrostatic contribution of the solvation free energy can be calculated with the PB equation-based implicit membrane model. The non-polar contribution of the solvation free energy is often approximated with a function that depends linearly on the solvent-accessible surface area of the molecule ,31,32. ATo evaluate the effectiveness of various treatments for fixed singular charges and compare the performance of different methods, we first solve the Poisson equation (corresponding to the zero ionic strength case in PB model) for a single atom model without membrane, which can be solved analytically. In this model, we use a sphere with a radius The analytical form of the electrostatic solvation energy for a single atom in the bulk with an ionic concentration In this case, the electrostatic solvation energy is We explored three methods to solve the single atom model. The results are shown in A conventional method to improve the accuracy of numerical calculations is to continue to refine the mesh. However, this strategy may not work well to the point charge distribution as in our case due to existent singularities in the solution as showed The counter-intuitive observation of finer meshes with higher errors are, in our opinion, due to singular charges. In theory, the potential at the position of the singular charge is infinite. The electrostatic solvation energy was calculated in the solvated state and reference state (vacuum state). However, this potential becomes finite in numerical simulation. We have to approximate the real solution by the refinement of the mesh. Given the relative error of two iteration potentials in the numerical calculation, the numerical magnitude of the solution is larger  as the mesh becomes finer, and the absolute error of the iteration potentials become larger too. The electrostatic solvation energy may be more erroneous from calculating the difference between two larger values (the difference can be magnified by the absolute error). The final electrostatic solvation energy is the balance between the relative error and the absolute error of the iteration potentials. Please see the broken line graph As shown in As shown in In We consider a DNA molecule model possessing 778 atoms and −22 G, a harmonic component H and a regular component K is the number of atoms in the molecule, and H at the i-th point charge, respectively.The presence of the singular charge distribution in Equation  indicateThe electrostatic energy of periodic and non-periodic systems should converge as the box size is extended toward infinity as shown in Gramicidin A (PDB code: 1MAG) is one of the most widely studied ion channels. It forms aqueous pores in lipid bilayers that selectively pass monovalent cations. Gramicidin A is a small 15-amino-acid z-axis direction). The ion channel (red) goes through the span of the membrane.The triangle surface of the gA is generated by TMSmesh and the tetrahedral mesh is generated with Tetgen . Figure To explore the important role of the channel/pore recognition, we compare models containing different heights of the incorrectly added membrane in the pore region (HMP) with correctly recognized pore region (assigned with high dielectric constant as in solvent). As shown in The solution of Equation  yields tEquation :(2)ΔGsoli-th atom, z direction in the membrane environment.The non-polar part on model :(3)ΔGnp=Once T. i-th ion specie with valence The PB equation is widely used to consider continuum electrostatic interactions in implicit solvation models. Its general form readsThe solution of the PB equation yields the electrostatic contribution . Therefore, we take the Dirichlet boundary condition shown in Equation (x and y axes) on the side faces of the central box.The periodic boundary condition, in fact, mimics an infinitely periodic lattice, wherein the computation grid represents the central cell . In the Equation  on the tThe main idea in the FEM is to represent a domain with smaller subdomains called finite elements. The distribution of the primary unknown quantity inside an element is interpolated based on the values at the nodes or at the edges. The assembly of all elements results in a global matrix system that represents the entire domain of the problem. The solution is obtained after solving the system. When dealing with Dirichlet boundary condition on the box, this constraint is applied directly to the linear system. However, for the lateral periodic boundary condition, the corresponding faces on the boundaries in the periodic direction are marked with the same label. Thus, they are treated as the same faces and shared by the two faces’ adjacent elements. In other words, the periodic boundary in FEM can be handled through “stitching” the boundary adjacent elements and treating them as normal interior elements (the boundary nodes share a same set of unknowns). The treatment mentioned above is illustrated in High quality surface and volume meshes form a necessary ground for numerical calculations, especially for the finite element calculation. The structures of biomolecules are highly complex. The addition of membranes increases the difficulty for the mesh construction. In this paper, we use a previously published method to generate meshes for implicit membrane solvation models containing membrane transport proteins . The difz-axis and the channel. In addition, in order to ensure that the lateral periodic boundary conditions to be realized by FEM, the mesh of the opposite box surfaces need to be consistent (one face can be considered as a copy of the other by translation) in the periodic direction. The limitation of the previous walk-and-detect method is the fixed detection directions. Now we improve it by walking in a random direction adaptively to adapt to the situation where the channel is not perpendicular to the membrane (x-y plane) but with a tilt angle between the Our FEM uses body-fitted mesh in which the mesh needs to conform to the molecular surface. The molecular surface triangulation is a demanding task in FEM simulations. TMSmesh ,38 and NWe employ two types of methods to treat the fixed singular charges: direct integral method and charge assignment method. The latter contains three different strategies.v at the position of Direct integral method: The fixed charges are singular points which may cause numerical difficulties. As in most finite difference treatments, the singular charges are assigned to neighboring grids, which is equivalent to taking a continuous approximation of the original singular distribution. Whereas in the FEM, the singular integral in the weak form Equation  actuallyj-th node. The basic idea in the FEM is to partition a domain into a number of non-overlapping elements (we use tetrahedrons in this paper), and to approximate the solution over each element by means of a selected set of basis functions. The simplest basis functions are piecewise linear functions, in which the four vertices of a tetrahedron are used as control points. In each element, we can express the dimensionless potential u asu at the i-th vertex of the element. The basis functions i-th vertex but 0 at the other three vertices. Once the coordinate of unknown u is confirmed, we can calculate the corresponding barycentric coordinates i-th vertex and the entire tetrahedron  Vertex-on-charge method: A direct thought is to constrain the mesh vertices on the fixed charges (by adding extra constrained points when using Tetgen ). In thi(2) Average assignment method: A simple idea is to assign each charge equally to the neighboring vertices within a truncating sphere radius. Suppose a charge Thus, the assigned charge (3) Weighted assignment method: It is unreasonable that all the nodes in the intercepting distance play the same role in the average assignment method. A weighted assignment method can be an improvement.j-th vertex of the i-th assigned charge. Therefore, all the assigned charges need to be scaled by a factor Inspired by the vertex-on-charge method, it is quite clear that we can assign the fixed charge The vertex-on-charge method needs a special treatment in the process of mesh generation. Otherwise, it may cause poor mesh quality. The average assignment method does not need to determine which elements the fixed charges are in but it ignores the different influences of different related nodes. The weighted assignment method takes the difference of grid node into consideration at a computational cost. In this paper, we compared the accuracy of the latter two methods with the direct integral method in the Result section.In this paper, we present a finite element method for PB electrostatics calculations of the membrane channel systems with periodical boundary condition (FEPB). To verify the correctness of the program for FEPB, especially for the treatment of the fixed singular charges, we compare three strategies in the single atom model with the analytic solution and arrive at the conclusion that proper mesh refinement can improve the computational accuracy. In the process of exploring the appropriate mesh size for the FE calculations using direct integral method to treat the fixed singular charges (without charge assignment), a mesh resolution about 0.36 Å is recommended in FEM  for a nearly optimal accuracy in the mesh construction. Further refinement may increase the relative error.The effect of lateral periodic condition is shown to be significant when the box size is at the same order of channel protein size. In the model of the DNA molecule without membrane, The results of decomposition and non-decomposition methods with non-periodic boundary condition are very close. This further verifies the feasibility and applicability of the non-decomposition method. At the same time, the results of APBS calculation are consistent with our calculations.In the application of lateral periodic boundary conditions in the channel protein, the ion concentration in the bulk plays a relatively less important role in the solvation calculation of channel proteins relative to the thickness of membrane. Solvation energy tends to increase as the membrane gets thicker especially for low The non-polar contribution to solvation energy in the membrane environment has also been incorporated into the PB model to calculate the total solvation energy. The estimation of the the tilt angle of the channel protein is a bit rough. More factors and more accurate non-electrostatic solvation models are needed for this type of studies.The related meshing tools and the solver FEPB are going to be available and can be executed at the online scientific computing platform: xyzgate.com.


This paper proposes a composite channel virtual time reversal mirror (CCVTRM) for vertical sensor array (VSA) processing and applies it to long-range underwater acoustic (UWA) communication in shallow water. Because of weak signal-to-noise ratio (SNR), it is unable to accurately estimate the channel impulse response of each sensor of the VSA, thus the traditional passive time reversal mirror (PTRM) cannot perform well in long-range UWA communication in shallow water. However, CCVTRM only needs to estimate the composite channel of the VSA to accomplish time reversal mirror (TRM), which can effectively mitigate the inter-symbol interference (ISI) and reduce the bit error rate (BER). In addition, the calculation of CCVTRM is simpler than traditional PTRM. An UWA communication experiment using a VSA of 12 sensors was conducted in the South China Sea. The experiment achieves a very low BER communication at communication rate of 66.7 bit/s over an 80 km range. The results of the sea trial demonstrate that CCVTRM is feasible and can be applied to long-range UWA communication in shallow water. Due to their multipath interactions, UWA channels are considered one of the most challenging wireless communication environments. The slow sound speed, the sound absorption and the variability of water can produce serious interference in UWA signals. Especially in shallow water channel , specifiTRM can be used for time compression and spatial focusing, making channel equalization and multipath interference reduction come true, in the absence of any prior knowledge , so it iIn summary, ATRM is both expensive and difficult to implement, and is not practical, while PTRM can obtain the same theoretical performance in a simple way. Nevertheless, PTRM needs to estimate the channel impulse response of each sensor of the VSA, which is somewhat unrealistic in complex long-range shallow water environments, because the SNR of the received signals of each sensor is too weak to estimate the channels accurately. Therefore, this paper proposes a CCVTRM technology for UWA communication and makes some theoretical derivations of this technology. The proposed method utilizes the spatial gain of the VSA to estimate the single composite channel, thus implementing the CCVTRM and achieving the temporal focusing. A long-range communication experiment in shallow water conducted in the South China Sea validates the practicability of this technology.Pattern time delay shift coding scheme ,25 is a T0 denotes the length of one symbol. The encoding time window for information coding is As shown in In a long-range shallow water environment, it is always impossible to estimate the channel pulse response of each sensor to implement traditional PTRM because of the low SNR. Although the array signal processing (ASP) can achieve spatial gain, the ISI resulting from multipath propagation in shallow water cannot be suppressed. In view of this, CCVTRM is put forward to improve the VSA processing. The point source (PS) transmits a probe pulse signal During the long-range UWA communication in shallow water, the SNR of received signals of each receiver is so low that Combining Equations (3) and (6), the composite channel can be expressed as:The function ASP makes the direct sounds of each sensor coherently superimposed and provides a higher SNR to the output signals To calculate the output SNR gain of CCVTRM, given that the SNR of each path signal is equal and noises are uncorrelated in the array elements, we can obtain:The output SNR is:Combining Equations (12) and (14), we can obtain:Thus, the SNR gain of CCVTRM is:As we can see in Equation (16), the more complex the multipath, the higher SNR gain of CCVTRM we can obtain. In a word, CCVTRM for the VSA processing not only has a simple calculation, but also gets the spatial gain from the VSA and the temporal focusing gain from TRM, moreover, it can mitigate the ISI caused by multipath.The key to implementing CCVTRM is detecting the probe pulse signal and estimating the composite channel. From the signal processing point of view, copy-correlation can be viewed as a matched filter that can achieve a maximum SNR under ideal conditions. In this paper, copy-correlation technology is used to detect the probe signal and estimate the composite channel.In the absence of multipath, the output probe signal of the VSA can be expressed as:After copy-correlation processing, the output is:Because the probe pulse signal and the noise are uncorrelated, the noise component is weak. Consequently, a correlation peak can be easily found at Taking multipath into account, Equations (17) and (18) can be modified as:It can be seen that the output of copy-correlation contains multiple correlation peaks and the positions of the peaks corresponding to time delay of the multiple paths. Considering the effects of noises, we set a threshold and keep the peaks that higher than the threshold. Then the channel impulse response is obtained.A long-range UWA communication experiment using CCVTRM was conducted in the South China Sea. The procedure started with sending a probe signal to estimate the composite channel of the VSA, followed by the data stream. Both the probe signal and the data stream were using LFM signal form with a bandwidth of 500–800 Hz. And the sampling rate was 48 kHz at both the transmitter end and the receiver end. Trials at different communication rates were conducted by adjusting the pattern pulse width and the length of the encoding time window. As can be seen in Since UWA channel is rapidly time-varying, the duration of signal frame should be short. In this case, we transmitted 196 bits of information data in each communication trial and changed the communication rates. In view of the complex environment of long-range UWA communication in shallow water, this paper proposes a CCVTRM for the VSA processing to improve the performance of UWA communication. Using the VSA can obtain a certain spatial gain and enhance the SNR of received signals, which is good for the UWA signal processing. As well as the general ocean acoustic channels, the composite channel of the VSA has complex multipath structure and wide time delay spread, resulting in severe ISI and high BER. For the array processing, CCVTRM can effectively reform the multipath structure of the composite channel and get the energy focusing gain, so as to mitigate the ISI and reduce the BER. The UWA communication experiment achieves a low BER communication at communication rate of 66.7 bit/s over an 80 km range, demonstrating the practicability and robustness of CCVTRM. It turns out that this technology can be applied to long-range UWA communication in shallow water.


Bearing fault features are presented as repetitive transient impulses in vibration signals. Narrowband demodulation methods have been widely used to extract the repetitive transients in bearing fault diagnosis, for which the key factor is to accurately locate the optimal band. A multitude of criteria have been constructed to determine the optimal frequency band for demodulation. However, these criteria can only describe the strength of transient impulses, and cannot differentiate fault-related impulses and interference impulses that are cyclically generated in the signals. Additionally, these criteria are easily affected by the independent transitions and background noise in industrial locales. Therefore, the large values of the criteria may not appear in the optimal frequency band. To overcome these problems, a new method, referred to as multiband envelope spectra extraction (MESE), is proposed in this paper, which can extract all repetitive transient features in the signals. The novelty of MESE lies in the following aspects: (1) it can fuse envelope spectra at multiple narrow bands. The potential bands are selected based on Jarque-Bera statistics of narrowband envelope spectra; and (2) fast independent component analysis (fastICA) is introduced to extract the independent source spectra, which are fault- or interference-related. The multi-band strategy will preserve all impulse features and make the method more robust. Meanwhile, as a blind source separation technique, the fastICA can suppress some in-band noise and make the diagnosis more accurate. Several simulated and experimental signals are used to validate the efficiency of the proposed method. The results show that MESE is effective for enhanced fault diagnosis of rolling element bearings. Bearing faults can be detected even in a harsh environment. Rolling element bearings (REB) are widely used in rotating machinery. Unexpected faults occurring in bearings may lead to fatal breakdown of machines and result in enormous economic losses in industry. Therefore, it is important to accurately detect defects in bearings early. Vibration signals are widely used for bearing fault diagnosis ,2,3. WheEnvelope analysis is able to highlight the fault characteristic frequencies of vibration signals, which have been widely used in bearing fault diagnosis . Since fThe problem of fault feature extraction can also be solved by the narrowband amplitude demodulation method, which is a combination of band-pass filter and envelope analysis. Narrowband demodulation methods offer, strong and reliable diagnostic potential, since they are based on a solid physical background, which can greatly improve the SNR. There are two key issues in narrowband demodulation: the design of the filter to segment the signal, and the construction of criteria with which to determine the informative frequency band. The idea of applying kurtosis for sub-signals introduced by Antoni  has captSince kurtosis of temporal signals can be considerably affected by noise and large random impulses, Barszcz and Jabłoński  recentlyCriteria constructed on the envelope spectrum are efficient for discovering the periodic repetitive impulses in a signal. However, it is hard to determine the fault-related resonance band via the values alone, since the criteria are particularly vulnerable to the impact of casual impulses. For example, periodically generated interference impulses are also converted to impulses in the envelope spectrum and lead to a large criterion value. In circumstances with heavy interferences, large criterion values can appear in several frequency bands, and the largest criterion value may not appear in the optimal band. Hence, selecting a signal in only one frequency band may leave out quite a few transient features, and a multi-band strategy is more robust since it can retain all potential bands. Considering the merits of criteria calculated using the envelope spectrum and multi-band strategy, a novel method named multiband envelope spectra extraction (MESE) is proposed in this paper. The proposed method can extract all narrowband envelope spectra with repetitive impulse components in the signal, which can be used to detect characteristic frequencies of the faulty bearing. Simulation and experimental results demonstrate that the proposed method is more accurate and robust than the narrowband demodulation methods in bearing fault diagnosis.JB) statistics is also described in this section. Simulation analysis of the proposed method is discussed in The remainder of this paper is arranged as follows. JB statistics is proposed. Finally, envelope spectra at multiple bands are selected, and fast independent component analysis (fastICA) is introduced to extract the impulsive source spectra in these narrow bands. The details are described in the following subsections.The proposed method is divided into several steps in this section. Firstly, the frequency band segmentation process is introduced. Then, a band determination technique based on the The signal is split into segments in the frequency domain, and the criterion based on envelope spectrum is calculated. The band segmentation process can be explained as a rectangular window with the length of the bandwidth truncating the frequency series. Central frequencies of the window that shift over the frequency range are determined by the bandwidth and shift step, which are the two most crucial parameters in this technique. It is a simple but effective way to intercept the frequency band and to obtain the narrowband signals. The flowchart is depicted in x(k) , N is the length of the discrete series. In the segmentation process, the signal is first transformed to the frequency domain by discrete Fourier transform (DFT) [X are Fourier coefficients of the signal. Then a rectangular window is defined to truncate the frequency series:BW is the length of the window. Frequency band segmentation is realized by slipping the window over the frequency series.iX are Fourier coefficients of the ith segment and a is the shift step length or iteration step length. Then, the frequency segment series SX can be expressed asm is the number of segments, which is determined by the length of the discrete series N, window length BW and shift step length a.Suppose the acquired vibration signal is a time series rm (DFT) ,23.(1)Xa and window length BW have a significant influence on the determination of SX, which should be carefully picked.The symbol ⌊ ⌋ in Equation (5) means to get the maximum integer that is not more than the operated data. The shift step length SX is obtained, the criterion of the envelope spectrum amplitudes in each narrowband should be calculated. Each frequency segment is firstly transformed into the time domain by inverse Fourier transform. The envelope of the sub-signal in each narrow band can be obtained by Hilbert transform (HT) [ieX is obtained through fast Fourier transform (FFT) of the envelope. Thus, the acquired envelope spectrum series can be expressed asAfter the frequency segment series orm (HT) ,24. ThenPeriodic repetitive transient impulses in the time signal can bring impulses in to the envelope spectrum. Therefore, the next step is to identify these narrow bands with impulsive envelope spectra.ith narrow band, kurtosis [ieX is defined asKurtosis of the envelope spectrum can well reflect the impulsiveness of signal. For the kurtosis  of its eIn the existing methods ,15,17,18JB statistic of the envelope spectrum to determine the candidate bands as it performs better than kurtosis in the detection of impulsiveness [In bearing vibration signals, fault-related features are presented as repetitive transient impulses. Since energies of impulses in the time signal spread over a wide frequency range, bearing fault features may be contained in narrowband signals with different central frequencies, which are presented as impulses in the envelope spectra. To verify the characteristics of repetitive impulses presented in the bearing fault signal, a real fault signal with small noise is analyzed in this section. siveness .JB statistic is a combination of empirical skewness and kurtosis, and has been used to test whether sample data match a Gaussian distribution. For the ith narrow band, the JB statistic [ieX is defined asiS is skewness of the envelope spectrum ieX and can be calculated asThe tatistic  of the eJB statistic in band determination, a few simulated envelope spectra are generated, as per [JB statistic (JB in the figure) and kurtosis (K in the figure) are calculated for comparison and presented at the top of each sub-figure. As can be seen in the figure, the value of the JB statistic varies dramatically when harmonics are present in the spectrum. However, for the spectra with or without harmonics, the values of kurtosis change very little, since they have the same order of magnitude. Hence, JB statistic is more sensitive than kurtosis in harmonics detection in the narrowband envelope spectrum, which can make the criteria of these bands with impulse features more protruding in the criterion series. Since the threshold for separating informative bands and bands dominated by noise is defined based on all of these values of the criterion, the protrusion can make the process more accurate.In order to evaluate the performance of , as per . The harJB statistic of every narrowband envelope spectrum, the criterion series is obtained as iJB . Since values of JB statistic can be indicative of the impulsiveness of a narrowband signal, the mean of the JB statistic series expressed as JBT is calculated as the threshold. This threshold is used to filter out those bands whose envelope spectra are drowned in noise.After calculating the JB statistics bigger than JBT are selected to form the informative spectra series Y = {Y1, Y2, …, hY} (where iY is envelope spectrum of the ith selected band). All these narrow bands are potential bands where transient impulses occur, but in which the envelope spectra may also be masked by noise.The envelope spectra of these narrow bands with Y1, Y2, …, hY are assumed to be linear combinations of l unknown independent spectra E1, E2, …, lE (l ≤ h). iE is the ith pure source envelope spectrum related to repetitive transient impulses. Let us arrange the spectra iY into a vector Y = T and the source spectra into another vector E = T, respectively. Then, the linear relationship is given byA is an unknown h × l matrix, which is referred to as a mixing matrix, and tN is random noise. The basic problem is to extract the source spectra E from the selected spectra Y or, equivalently, to estimate the mixing matrix A. This is a blind source separation (BSS) problem.As described in the last subsection, the bands with criteria bigger than the threshold have envelope spectra containing impulses, which correspond to repetitive transient impulses cyclically generated in the time signal. These impulses are caused by a bearing fault or interference that can be distinguished by frequency components in the spectra. The informative spectra may contain fault-related features, inference-related features, or both. Therefore, each selected spectrum is a combination of a fault-related spectrum and an interference-related spectrum. The pure fault spectrum and interference spectrum both have definite shapes that contain impulses with regular intervals. In the simplest form, the selected spectra There are several algorithms to solve BSS problems, such as Jutten-Hérault algorithm , nonlineY consists of finding a linear transform matrix W to make the components E = TYW as independent as possible, in the sense of maximizing some function that measures independence. ICA is usually performed by formulating an objective function, which is also called a contract function, and then minimizing or maximizing it. The two key factors for fastICA or ICA are source number estimation and the definition of contrast function, which will be discussed next. The following gives a succinct description for ICA and fastICA used in our method.The fastICA is an improved method of ICA, and has the same principle as ICA. ICA of the vector y = T, negentropy [gaussy is a Gaussian random vector that has the same covariance matrix as y. H(.) is the differential entropy of the vector and is defined asyp(.) is the vector’s possibility density. Negentropy is always non-negative, and is zero if and only if y has a Gaussian distribution. Finding a transformation matrix to extract source data is roughly equivalent to finding the projection directions in which the negentropy is maximized. It is impossible to get the possibility density of the vector in real cases. Therefore, a simple estimate of the negentropy is needed. Many approximations have been developed [c is a constant, v is a Gaussian variable of zero mean and unit variance, and g is a nonquadratic function. In this study, the function is defined asb ≤ 2 is constant. The approximation formula can give a new objective function to estimate the ICA transform. To find one source spectrum iE = iTYW in this study, the projection direction can be obtained by maximizing the function gJ given byIn this study, the ICA problem is solved by negentropy maximization. Negentropy can be interpreted as a measure of nongaussianity. For a vector gentropy  is defineveloped  based oni*W denotes the new value of iW. The iteration can be used to optimize the matrix W and separate these independent source spectra.As an optimization process, the independent components can be estimated one by one. In fastICA, the fixed-point iteration algorithm that computes in batch mode is introduced to maximize the objective function and makes the convergence fast and reliable. After some reasonable approximations, it can obtain the following iteration :(17)Wi+=h ≥ l. Therefore, the number of source spectra in the signal needs to be accurately estimated. As these observed vectors will formulate a high dimension matrix, it is a dimension reduction process and can be realized by a PCA-related method. The main step in PCA is to calculate the covariance matrix of the original data and find out the eigenvectors and eigenvalues of the matrix. The problem of detecting the number of sources is equivalent to determining the number of source eigenvalues. The rearranged eigenvalues can be expressed asIn this study, the extraction of source envelope spectra is an overcomplete ICA problem, such as There are many kinds of indexes ,34,35,36id will be small when iλ and iλ+1 are both noise eigenvalues, but large if one or both are source eigenvalues. This suggests that estimating the number l is equivalent to estimating the multiplicity of the eigenvalues. The test starts checking the difference of adjacent eigenvalues from i = 1. When the difference is less than the alarm threshold ε, the detection scheme is over, which corresponds to the interface between the signal and noise subspaces. As a result, we get the ideal source number estimation.The shapes of source spectra are different from each other, while the same source spectrum appeared in multiple narrow bands often has definite shape. The difference After getting the number of independent source spectra and defining the contrast function, the main steps of fastICA are given as follows:Step 1: Center and whiten the measured data Y;Step 2: Estimate the number of source l in the system based on differences of adjacent eigenvalues and let p = 1;Step 3: Choose a random initial vector PW with norm 1 and determine the loop’s termination condition;Step 4: Let g(.) is the nonquadratic function as Equation (15) and g′(.) is the derivative of g(.);Step 5: Perform Gram-Schmidt orthogonalization to achieve decorrelation:Step 6: If the iteration is not convergent, go back to step 4;Step 7: Let p = p + 1. If p ≤ l, go back to step 3. Otherwise, output the optimal matrix W, which is constructed by all the vectors iW.JB statistics of narrowband envelope spectra, as introduced in JB statistics is calculated as the threshold. Envelope spectra of the selected narrow bands can be seen as observed data in BSS, and the source data are truly impulse-related spectra. Finally, the fastICA algorithm is used to extract the source envelope spectra, and the number of source spectra is determined by differences of adjacent eigenvalues. These source spectra contain features for bearing fault diagnosis.Based on the above discussions, the procedure of the proposed method for detecting REB faults can be briefly described in x(t) can be computed by the following formulas(t) is the oscillating waveform, n(t) is Gaussian white noise, jA is the amplitude of the jth impulse. M is the number of impulses and T represents the time period corresponding to the characteristic frequency. In the above equation, s(t) is defined asβ is the damping coefficient, rf is modulation frequency, which reflects the resonance information of the system. The value of jA is related to the location of the defect in rolling element bearings [cf of the simulated bearing fault is 200 Hz. There will be about 65,000 samplings in the simulated signal, but only 4000 of them are shown in the figure to display clearly. The simulated signal and the pure impulses with red lines are presented in cf and its harmonics are not evident in the spectrum.In the simulation, the fault signal is modeled as a series of repeated damping oscillation waveforms . It is abearings  and is sJB statistics of narrowband envelope spectra are presented in cf are quite effectively extracted. Sub-figures in MESE is used to analyze the signal presented in rf1 (6000 Hz) and characteristic frequency cf1 (260 Hz) to the simulated signal above. Rotational frequency Rf of the sinusoid is 50 Hz, and the amplitude is 1.0 in this case. The simulated signal and its envelope spectrum are presented in In industrial locales, quite a few other repetitive transient impulses periodically excited by mechanical elements may also appear in the signal, and these comprise the interference impulse components. Meanwhile, sinusoids brought in by the shaft machine are familiar in vibration signal. Hence, we also simulate the REB fault signal with these two interferences. The impulse interference can be easily realized by adding another impact signal with resonance frequency JB statistic is displayed in JB statistic. If only the band with the biggest criterion is selected for further analysis, the fault-related features will not be detected. The criterion diagram can be more complicated in real cases, which need more manual intervention to choose the right frequency band for demodulation and will complicate the fault diagnosis. In MESE, multiple discrete narrow bands are selected for further analysis. To verify the effectiveness of the proposed method in practical applications, we established a simplified bearing test rig, which is shown in It may be impossible to mount sensors near the failure bearings in quite a few situations of industrial field, so fault diagnosis by signals acquired at long distance is meaningful in practical applications. In the experiment, we simulated situations in which the measuring points were far away from the defective bearing. Three accelerometers were mounted along the shaft at Point 1, Point 2 and Point 3 to acquire vibration signals, as shown in The type of tested bearing is HRB 6010-2RZ , and parameters of the bearings are listed in If is 185 Hz in this condition. The temporal waveforms and corresponding envelope spectra are illustrated in If are flagged with vertical red dashed lines for a clear view. If. Therefore, signals measured at Point 1, Point 2 and Point 3 are in situations with low interference, medium interference and heavy interference, respectively.As rotation speed is kept constant at 1500 rpm, the characteristic frequency of inner-race defect To verify the effectiveness of MESE in bearing defect identification, Protrugram  and the If are significantly enhanced, which can strengthen the visual inspection ability. Although the three methods mentioned above are effective in detecting the bearing inner-race defect in the experiment, spectrum obtained by MESE is the clearest to show the inner-race fault characteristic frequency and its harmonics.Rf is 25 Hz and the characteristic frequency of outer-race defect Of is 140 Hz. We also measured vibration signals at Point 1, Point 2 and Point 3 using accelerometers. The time signals and corresponding envelope spectra are displayed in For this test, the rotational frequency The fast Kurtogram and Protrugram are also introduced to analyze the signals for comparisons. Bandwidth of Protrugram is set to 500 Hz, which is slightly more than three times the sought characteristic frequency. The bandwidth for MESE is chosen to be 600 Hz. Analyzed results of the signal measured at Point 1 are presented in Of components cannot be found in the spectra. The envelope spectrum achieved by Protrugram is dominated by rotational components Rf, which may be the main interference in the signal. Two independent source spectra are obtained by the MESE method, as exhibited in Rf and the main components of the spectra lines in the 2nd spectrum are the outer-race characteristic frequency Of and its harmonics. Since the fault characteristic components are clearly identified, the method can successfully detect the defect in bearing outer race. It also can be concluded from the results that the main interferences affecting bearing fault diagnosis are rotational components in the signal.Analyzed results of signal measured at Point 2 are presented in Of components are not evident in the spectra. MESE extracts three independent source spectra, as shown in Of and its harmonics are clearly identified, which means MESE has outstanding performance in outer-race defect identification. All the results in this subsection indicate that the proposed method has an enhanced performance in outer-race fault diagnosis even in heavy interference situations.The analyzed results of the signal measured at Point 3 are presented in In this section, several real bearing fault signals are analyzed by the proposed MESE method, the fast Kurtogram method and the Protrugram method. These signals are measured at different points along the shaft to simulate situations with varying degrees of interference. For the signals measured near the tested bearing, although all three methods can successfully detect the two different kinds of bearing faults, MESE has the best visual inspection ability. When signals are measured far from the tested bearing, the fast Kurtogram and Protrugram have weak performance in fault diagnosis. In the case of outer-race defect, these two methods even fail to provide any bearing fault signatures in the extracted envelope spectra. However, the envelope spectrum obtained by MESE could clearly show the fault characteristic frequency and its harmonics both in the inner-race defect and outer-race defect situations. After the comprehensive comparisons were done, MESE showed the best performance among the three methods for bearing defect identification in our case studies. Therefore, the proposed method is effective and robust in bearing fault diagnosis.In narrowband demodulation, criteria used to determine the optimal frequency band are easily affected by some other interference components in the vibration signal. Therefore, selecting signal just in one frequency band may lead to inaccurate results in extracting the fault transient components. To overcome these shortcomings, this paper proposes a method of multiband envelope spectra extraction for enhanced bearing fault diagnosis. This method is inspired by the characteristics of the repetitive transient impulses presented in the bearing fault signal: (1) repetitive transients are present as impulses in envelope spectrum, which can lead to high values of criteria; (2) repetitive transients are spread over a wide frequency range, so the fault components appear in multiple narrow bands. The method is implemented by fusing the envelope spectra at multiple narrow frequency bands. These informative frequency bands are determined by Jarque-Bera statistics of envelope spectrum amplitudes. Fast independent component analysis is introduced to extract the fault-related source spectra in the selected bands. Since all impulse features are preserved, the diagnosis is more robust and accurate. Comparative studies on the simulated and real bearing signals indicate that the proposed method outperforms the fast Kurtogram and Protrugram in fault diagnosis. The experimental results show that the proposed method is able to extract fault-related signatures from signals with heavy interferences and is an effective and reliable method for rolling element bearing faults diagnosis.


Sample preparation is one of the most important steps in metabolome analysis. The challenges of determining microbial metabolome have been well discussed within the research community and many improvements have already been achieved in last decade. The analysis of intracellular metabolites is particularly challenging. Environmental perturbations may considerably affect microbial metabolism, which results in intracellular metabolites being rapidly degraded or metabolized by enzymatic reactions. Therefore, quenching or the complete stop of cell metabolism is a pre-requisite for accurate intracellular metabolite analysis. After quenching, metabolites need to be extracted from the intracellular compartment. The choice of the most suitable metabolite extraction method/s is another crucial step. The literature indicates that specific classes of metabolites are better extracted by different extraction protocols. In this review, we discuss the technical aspects and advancements of quenching and extraction of intracellular metabolite analysis from microbial cells.  Metabolomics can be described as a group of techniques applied to detect, identify and potentially quantify small organic molecules <1.5 kD) produced or modified by living cells .5 kD pro,3,4,5. I−1) when exposed to factors such as temperature and light  acetic acid in order to evaluate the quenching efficiency of this method, which proved to be very satisfactory. Other methods may be modified and adapted for quenching the cells of different species.As with filamentous fungi and protozoa, the cell envelope of microalgae is also diverse and may be very complex according to the developmental stage. Bolling and Fiehn (2005) modified the quenching method developed by de Koning and van Dam (1992) for quenching the metabolism of the microalgae nhardtii . They spE. coli) using a high-resolution mass spectrometer (time of flight) has been published by Link et al. [Many factors may influence the efficiency of a quenching method. Within these, the time between sampling and the actual quench of the cell metabolism is considered one of the most important. Because the inter-conversion of metabolites may happen in the order of seconds, a quick sampling and quenching method is essential for producing an accurate picture of the in vivo cell metabolism. Recently, a direct sampling method for the real-time metabolome profiling of bacterial cells   and afteE. coli. The main idea consisted of continuously spraying culture broth samples into sample tubes filled with quenching solution that moved at a defined speed underneath the bioreactor. The authors used a magnetic pinch valve inserted in the bottom of the bioreactor pointing to a magazine located underneath. This magazine had the capacity to horizontally transport 16 quenching tubes. As a result of the higher pressure inside the bioreactor, when the magnetic valve was opened, it continuously sampled culture broth at 3.3 ml s−1 into each individual sample tubes containing cold quenching solution moving underneath the bioreactor. This system allowed a sampling rate of 4.5 samples per second. Many other systems have been developed using similar technology [It was not until 1998 that the first fully-automated system for harvesting and quenching microbial cells was built . Schaefechnology ,68,69. EWhen studying the dynamics of the cell metabolism, a commonly applied strategy is called stimulus-response or continuous perturbation experiments ,64,66. IStimulus-response experiments can be performed using the fast sampling systems described above. However, it has some drawbacks when multiple stimuli are to be studied. Every stimulus must be applied when the cell culture reaches the steady-state condition. However, when the first perturbing agent is introduced into the cell culture, the culture steady-state is lost and, depending on the organism under study and the dilution rate applied, it may require more than 48 h and many litres of media to reach a new steady-state. In addition, there is a time frame required for the perturbing solution to mix with the cell culture and actually affect the metabolism of all living cells in the bioreactor. This time frame depends on the stirring speed, the volume of the culture and the viscosity of the liquid. Finally, the high volume of the bioreactors requires a large amount of perturbing agent, which may increase significantly the overall costs of the experiment. A solution for these limitations is presented by the sampling systems called stopped flow. These systems rely on applying the desired perturbations in a secondary flask, or outlet, sitting outside the bioreactor. A defined volume of cell culture is driven to the outlet where the stimulus solution is simultaneously injected. The low volume of the secondary flask promotes a quick and uniform mix between the stimulus solution and the cell culture. In addition, as the whole pulse-response process happens outside the bioreactor, the steady-state is maintained and a new experiment can be subsequently performed in little time. An efficient stopped-flow sampling system must be able to sample and quench microbial cells at a high frequency and in a reproducible manner.Many different stopped-flow systems have been developed to date. In 1992, de Koning and van Dam proposed a stopped-flow system using a freeze quench device in order to analyze changes in glycolytic metabolites . However2/CO2 silicon membrane, which is more flexible for switching from aerobic to anaerobic conditions and requires lower to minimum maintenance.Visser et al. developed a stopped-flow sampling system that overcame this problem . The so-Different factors are directly responsible for the shape and strength of the cell envelope (structure and composition) of different microorganisms. The complexity of a microbial cell envelope mainly depends on the structural polymeric composition of the cell and the degree of cross-linking between these polymers and other cell-wall components. Therefore, the major resistance that needs to be overcome during the disruption of cell envelopes is the covalent chemical bonds between the structural components. Both mechanical and non-mechanical methods are widely used for cell envelope disruption . Table 2Mechanical disruption of the cell envelope can be affected by different factors, such as polymer concentration within the cell wall, cell size and shape and degree of cross-linking between the polymers. However, the ease of mechanical cell disruption depends on the complexity and composition of the cell envelope. For example, the cell wall of Gram-negative bacteria can be easily ruptured using mechanical methods when compared with the cell wall of Gram-positive bacteria. Similarly, the cell-wall composition of yeasts and filamentous fungi is more complex than that of bacteria; therefore, the disruption of their cell wall requires stronger mechanical forces . DiffereNon-mechanical cell enveloped disruption methods are generally preferred for the extraction of the intracellular metabolites from microorganisms. In this case, chemical or physical agents are used to make the cell envelope permeable so that the intracellular metabolites can be released into the cytoplasmic medium. Different disrupting agents, such as, enzymatic, mechanical and chemical, can be used for the preparation of intracellular samples. The application of both enzymatic and physical agents is quite limited in metabolomics because of their ability to degrade the polymeric components of the cell envelope and result in leakage of large molecules. Some of these enzymatic-physical methods can be combined with chemical methods to enhance the extraction process. Chemical lysis of the cell envelopes is part of the majority of protocols developed to extract intracellular metabolites from microbial cells . IdeallyThe most popular methods for intracellular metabolite extraction are based on the application of chemical agents . MetabolBoth polar  and non-polar  solvents are extensively employed for the extraction of microbial intracellular metabolites. The organic solvents have the ability to weaken the cell wall, cell membrane proteins and lipids; therefore, they can form pores in the cell envelope. Then the intracellular metabolites are released through the pore and extracted into the organic solvent. However, the ideal solvent-extraction methods should require a small of amount of solvent. In addition, the volume of sample, the extraction time and the broadness of the coverage metabolites are three other important parameters while choosing a suitable extraction protocol ,18,73. IThe use of buffered boiling ethanol (75% v/v) is a simple and rapid intracellular metabolite extraction protocol. This method was first reported by Entian et al.  and lateCold-methanol extraction is an extensively used method that is also another simple and fast method for the extraction of the intracellular metabolites from a wide range of microbial cells. For instance, cold methanol has been used to extract metabolites from bacteria ,73,74, y−40 to −20 °C) while shaking the mixture vigorously (about 300 g for 45 min) to extract polar metabolites of yeast cells. This method is highly useful for the extraction of both polar and non-polar metabolites from bacteria, yeasts and filamentous fungi. Thermo-labile metabolites can also be extracted by this method as it is performed at a low temperature. Even though chloroform is known as a toxic and carcinogenic agent, it helps to denature all the enzymes within microbes and stops further chemical reactions. However, appropriate precautions need to be undertaken while using this method to avoid the hazardous effects of chloroform. In addition, it is a laborious and time-consuming method, and the buffers also may cause problems for different analytical techniques [The extraction of intracellular metabolites  from animal tissue using buffered methanol–chloroform–water was first reported by Folch et al. . Howeverchniques . Howeverchniques . E. coli using pre-heated de-ionized hot water . This method is advantageous because it is very simple and easy to perform. In addition, enzyme activity is more likely to stop because of the high temperature of the water. However, this method can only extract polar metabolites and is not suitable for thermo-labile metabolites. Hot water has been used for the extraction of bacterial amino acids since 1950s . Later oThe extraction of intracellular metabolites using acids  is one the classical methods that has been used for many years. This method is proved to be a good one for polar and acid-stable metabolites and has been used for the extraction of intracellular metabolites from bacteria, yeasts and filamentous fungi ,38,74,84Alkalis are mainly used for the extraction of intracellular metabolites from yeast and filamentous fungi. This extraction process is also carried out at a low temperature (0–4 °C) coupled with a freeze–thaw cycle. This is an excellent method to disrupt the microbial cell wall that deactivates enzymes promptly at extreme high pH. However, there are a few drawbacks to this method, which include poor recovery of intracellular metabolites, saponification of lipids and hydrolysis of proteins and polymers ,51. OnceAlthough many mechanical cell-disruption protocols  are widely used to extract the metabolites from plant and animal cells, these are not preferred methods for the extraction of microbial intracellular metabolites. However, two methods, such as supercritical fluid extraction (SFE) and pressurized liquid extraction (PLE) have been used for the extraction of intracellular metabolites from some microorganisms. We will briefly discuss their application to microbial systems in following sub-sections.SFE allows the extraction of non-polar to mid-polar compounds from bacteria, yeast and filamentous fungi . This mePLE is mainly used for the extraction of secondary metabolites produced by the microorganisms. However, this method has not been used by many researchers in the field of metabolomics. But this method is suitable for high-throughput screening and very concentrated metabolite extracts can be obtained . On the Quenching is certainly one of the most crucial steps in metabolomics studies. An efficient quenching method for microbial cultures must be fast, reproducible, and it must prevent leakage of intracellular metabolites to the extracellular medium. Several quenching methods have been developed to date; however, each method shows a considerable specificity to the organism under study and the culture medium in use . Recently, very efficient fully automated systems have been developed to increase the sampling speed and reduce the variability introduced by human errors. However, they are mostly purpose-made and not commercially available. There is a need for more robust quenching methods and also more accessible equipment, which may be achieved by merging the knowledge of specialists from distinct fields, such as biology, chemistry and engineering. The standardization of analytical protocols and extraction methods is the most discussed topic among members of the metabololomics community. These discussions over the last decade make it clear that no single analytical technique is sufficient to determine the comprehensive metabolite profiles from biological samples; rather, a combination of different techniques has been suggested for acquiring as much information as possible. Similarly, recent work from different laboratories also raises general consciousness about the necessity of a global (and standard) extraction protocol that can be used to extract as many metabolites as possible. If that is not realistic or not achievable, then the combination of extraction methods by using solvents with different polarities would be very useful for obtaining global and more accurate intracellular metabolite profiles from microorganisms. In this way, we would be able to achieve a more precise biological interpretation of the metabolomics data.