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Radio-echo sounding (RES) is widely used for polar ice sheet detection due to its wide coverage and high efficiency. The multivariate variational mode decomposition (MVMD) algorithm for the processing of RES data is an improvement to the variational mode decomposition (VMD) algorithm. It processes data encompassing multiple channels. Determining the most effective component combination of the penalty parameter (α) and the number of intrinsic mode functions (IMFs) (K) is fundamental and affects the decomposition results. α and K in traditional MVMD are provided by subjective experience. We integrated the particle swarm optimization (PSO) algorithm to iteratively optimize these parameters—specifically, α and K—with high precision. This was then combined with the four quantitative parameters: energy entropy, signal-to-noise ratio (SNR), peak signal-to-noise ratio (PSNR), and root-mean-square error (RMSE). The RES signal decomposition results were judged, and the most effective component combination for noise suppression was selected. We processed the airborne RES data from the East Antarctic ice sheet using the combined PSO–MVMD method. The results confirmed the quality of the proposed method in attenuating the RES signal noise, enhancing the weak signal of the ice base, and improving the SNR. This combined PSO–MVMD method may help to enhance weak signals in deeper parts of ice sheets and may be an effective tool for RES data interpretation. [ABSTRACT FROM AUTHOR]

Geologic interpretation results from conventional ground-penetrating radar (GPR) detection methods tend to have a certain degree of uncertainty. In order to improve the reliability of ground-penetrating radars in the detection of rock mass fissures in grottoes, this study proposes a ground-penetrating radar detection method with the logging data constraint, which is applied to detect the fractured rock mass in the Baodingshan Scenic Area of Dazu Rock Carvings, Chongqing, China. First, conventional logging and borehole televiewer data were compared and verified, yielding detailed lithological and wellbore fissure information. Next, electromagnetic wave velocity was calibrated using GPR profile and the depth of the stratigraphic interface determined by borehole data. Utilizing this calibrated velocity, we are able to accurately calculate the depth values of anomalies in GPR interpretation profiles. Subsequently, we compared the preliminary GPR interpretation profile with the borehole televiewer images. After eliminating false anomalies caused by interference, we obtained more reliable location information for detection targets such as fissures, fracture zones, and weak interlayers. The results of fissure detection in the Dazu Rock Carvings indicate that the detection results of ground-penetrating radar are verified and supplemented under the constraints of stratigraphic and well-wall fissure information obtained by logging. This effectively mitigates the influence of multiplicity and false anomalies of GPR detection on interpretation results. GPR with the logging data constraint enhances the accuracy of the fissure detection results, providing novel technical means for the protection and restoration of grotto relics. [ABSTRACT FROM AUTHOR]

For the full waveform inversion, it is necessary to provide an accurate source wavelet for forwarding modeling in the iteration. The source wavelet estimation method based on deconvolution technology can solve this problem to some extent, but we find that the estimated source wavelet is not accurate and needs to be manually corrected repeatedly in the iteration. This process is highly operator-intensive, and the update process is time-consuming and increases the potential for errors. We propose a source-independent waveform inversion (SIEWI) scheme for cross-hole GPR data, and use the envelope objective function combined with this method to effectively reduce the nonlinearity of inversion. The residual field used by SIEWI to construct the gradient inherits the characteristics of the envelope wavefield. Compared with full waveform inversion (FWI), SIEWI is more robust and less sensitive to frequency components and inaccurate source wavelet. To avoid cycle jumping, the multi-scale strategy effectively utilizes the properties of convolutional wavefields. In one iteration, the wavefield is decomposed into multiple frequency bands through multiple convolutions in the time domain to construct a multi-scale inversion strategy that preferentially inverts low-frequency information. [ABSTRACT FROM AUTHOR]

Ground Penetrating Radar (GPR) has become a widely used technology in geophysical prospecting. The Variational Mode Decomposition (VMD) method is a fully non-recursive signal decomposition method with noise robustness for GPR data processing. The VMD algorithm determines the central frequency and bandwidth of each Intrinsic Mode Function (IMF) by iteratively searching for the optimal solution of the variational mode and is capable of adaptively and effectively dividing the signal in the frequency domain into the many IMFs. However, the penalty parameter α and the number of IMFs K in VMD processing are determined depending on manual experience, which are important parameters affecting the decomposition results. In this paper, we propose a method to automatically search the parameters α and K optimally by Particle Swarm Optimization (PSO) algorithm. Then the signal-to-noise ratio (SNR) and root-mean-square error (RMSE) are used to judge the best superposition of the IMFs for data reconstruction, and the process is data-driven without human subjective intervention. The proposed method is used to process the field data, and the reconstruction data show that this innovative VMD processing can effectively improve the SNR and highlight the target reflections, even some targets not found in pre-processing are also revealed. [ABSTRACT FROM AUTHOR]

Modeling plays an important role in engineering exploration. However, the traditional rectangular mesh cannot meet the requirement because the actual shape of the model may be very complex. Therefore, this paper chooses the Delaunay grid for modeling and applies this method to magnetic numerical simulation. At the same time, we make use of the advantages of the Delaunay grid and choose to use grid encryption technology in the boundary and complex area of the model. Then, the formula for calculating the magnetic anomaly of tetrahedron is deduced in detail, and the magnetic anomaly with surface fluctuation is calculated. For a synthetic data model, Delaunay grids with different densities are used to model and calculate surface anomalies. The two results are compared with the analytical solution of the model. The results show that the method has high accuracy. Then, the method is applied to the actual geological body modeling in the Jinchuan mining area. According to local needs, a three-dimensional model with inhomogeneous grid density is established and the surface magnetic field of the model is calculated. Finally, the simulation data are compared with the measured data. The results show that the Delaunay grid modeling method has strong applicability. [ABSTRACT FROM AUTHOR]

Directional borehole radar (BR) 3-D imaging is a challenging problem due to its limited observation space within a borehole. We present a linear prediction (LP)-based direction-of-arrival (DOA) estimation and a migration-based 3-D imaging algorithm for the directional BR, which is composed of a transmitting antenna and a uniform circular array including four small receiving antennas. Only the azimuth is estimated, while the elevation and the distance are included in the imaging process. LP is a useful tool for DOA estimation in the radar domain, but a single linear array (LA) has azimuth ambiguity in DOA estimation. The four receiving antennas are treated as two orthogonal uniform LAs. The combination of two arrays removes the ambiguity in DOA estimation. In addition, the moving window and the threshold-based estimation increase the calculation efficiency. According to the estimated azimuth angles, the measured signal at each depth is decomposed to the corresponding directions. Therefore, there is a time-series signal in each direction at each depth. After processing the measured signals at all depths, we obtain a 3-D data set that can be used for horizontal- and radial vertical-section displays. Then, the radial vertical-section data are processed by migration which transforms the time domain signal into a wavefield-based 3-D image. Simulated data from a fracture model are used to validate the algorithm, and the reconstructed image can reveal the real model well. It is concluded that the novel method we propose is an effective one with real-time processing capability. [ABSTRACT FROM AUTHOR]

: Fish under intensive rearing conditions experience various stressors which have negative impacts on survival, growth, reproduction and fillet quality. Identifying and characterizing the molecular mechanisms underlying stress responses will facilitate the development of strategies that aim to improve animal welfare and aquaculture production efficiency. In this study, we used RNA-seq to identify transcripts which are differentially expressed in the rainbow trout liver in response to handling and confinement stress. These stressors were selected due to their relevance in aquaculture production. Total RNA was extracted from the livers of individual fish in five tanks having eight fish each, including three tanks of fish subjected to a 3 hour handling and confinement stress and two control tanks. Equal amount of total RNA of six individual fish was pooled by tank to create five RNA-seq libraries which were sequenced in one lane of Illumina HiSeq 2000. Three sequencing runs were conducted to obtain a total of 491,570,566 reads which were mapped onto the previously generated stress reference transcriptome to identify 316 differentially expressed transcripts (DETs). Twenty one DETs were selected for qPCR to validate the RNA-seq approach. The fold changes in gene expression identified by RNA-seq and qPCR were highly correlated (R2 = 0.88). Several gene ontology terms including transcription factor activity and biological process such as glucose metabolic process were enriched among these DETs. Pathways involved in response to handling and confinement stress were implicated by mapping the DETs to reference pathways in the KEGG database. Accession Numbers: Raw RNA-seq reads have been submitted to the NCBI Short Read Archive under accession number SRP022881. Customized Perl Scripts: All customized scripts described in this paper are available from Dr. Guangtu Gao or the corresponding author. [ABSTRACT FROM AUTHOR]

A directional borehole radar consists of one transmitting antenna in the borehole and four receiving antennas distributed at equal angles in a ring. The receiving antennas can determine the depth and orientation of targets beside the borehole. However, the problem of target orientation determination and 3D imaging algorithms remains a technological challenge. The MUSIC (multiple signal classification) algorithm requires a peak search, so the accuracy of the operation is limited by the angle interval. Based on the MUSIC algorithm, the Root-MUSIC algorithm is proposed and implemented. By replacing the spectral peak search with calculating the roots of the polynomials greatly improves the orientation recognition accuracy. Finally, the results obtained using the above algorithm are verified with synthetic data and compared with the results of the MUSIC algorithm. The results show that both the MUSIC algorithm and the Root-MUSIC algorithm can achieve very good orientation determination and 3D imaging results. In terms of accuracy, the Root-MUSIC algorithm has an obvious improvement compared with the MUSIC algorithm. [ABSTRACT FROM AUTHOR]

A major QTL for resistance to Fusarium head blight (FHB) in wheat, Qfhs.ndsu-3BS, has been identified and verified by several research groups. The objective of this study was to increase the marker density in this QTL region using STS (sequence-tagged site) markers developed from wheat expressed sequence tags (ESTs) near Qfhs.ndsu-3BS. Because wheat chromosome 3BS and rice chromosome 1S are syntenous, the sequences of P1-derived artificial chromosome (PAC) and (or) bacterial artificial chromosome (BAC) clones covering the sub-distal portion of rice chromosome 1S were used as queries for a BLASTn search to identify wheat ESTs most likely near Qfhs.ndsu-3BS. Sixty-eight out of 79 STS primer pairs designed from wheat ESTs amplified PCR products from the genomic DNA of Triticum aestivum 'Chinese Spring'. Twenty-eight STS markers were localized on chromosome 3BS by aneuploid analysis. Six out of the nine STS markers that could be mapped in the T. aestivum 'Sumai 3'/T. aestivum 'Stoa' population had higher R2 and LOD values for this QTL than the most significant marker reported previously. Therefore, leveraging genome sequence information available in rice for wheat genetics is an effective strategy to develop DNA markers for Qfhs.ndsu-3BS, and this strategy may have broad applications for targeted mapping of other traits in cereal crops. [ABSTRACT FROM AUTHOR]

Ecological water replenishment (EWR) has been increasingly applied to the restoration and maintenance of wetland hydrological conditions across China since the beginning of the 21st century. However, little is known about whether EWR projects help protect and/or restore wetland ecohydrology. As one of the earliest and longest-running EWR projects in China, water has been released from the Nenjiang River into the Zhalong wetland since 2001. It is important to examine the ecohydrological effects of this EWR project. In this study, long time series remote sensing data were used to extract the water area, inundation frequency, and normalized difference vegetation index (NDVI) to explore how eco-hydrological conditions changed during the pre- (1984–2000) and post-EWR (2001–2018) periods in the Zhalong wetland. Results show that the inundation area decreased due to the reduced surface water inflow during the pre-EWR period. Similarly, monthly vegetation NDVI in the growing season generally exhibited a decreasing and an increasing trend during the pre- and post-EWR periods, respectively. In the post-EWR period, NDVI increased by 19%, 73%, 45%, 28%, 13% for the months of May through September, respectively. Due to EWR, vegetation growth in areas with low inundation frequency was better than in areas with high inundation frequency. We found that the EWR project, runoff, and precipitation contributed 25%, 11%, and 64% to changes in the NDVI, respectively, and 46%, 37%, and 17% to changes in inundation area, respectively. These results indicate that the EWR project has improved hydrological conditions in the Zhalong wetland. For further maximum benefits of EWR in the Zhalong wetlands, we suggest that implementing similar eco-hydrological projects in the future should focus on flood pulse management to increase the inundation area, improve hydrological connectivity, and create new habitats. [ABSTRACT FROM AUTHOR]

The directional borehole radar can accurately locate and image the geological target around the borehole, which overcomes the shortcomings that the conventional borehole radar can only detect the depth of the target and the distance from the borehole. The directional borehole radar under consideration consists of a transmitting antenna and four receiving antennas equally distributed on the ring in the borehole. The nonuniformity caused by the borehole and sonde, as well as the mutual coupling among the four receiving antennas, will have a serious impact on the received signal and then cause interference to the azimuth recognition for the targets. In this paper, Finite difference time domain (FDTD), including the subgrid, is applied to study these effects and interferences, and the influence of borehole, sonde, and mutual coupling among the receiving antennas is found. The results show that, without considering the sonde and the fluid in the borehole, the one transmitting and one receiving borehole radar system does not have resonance, but the wave pattern of the reflected wave will have obvious distortion. For the four receiving antennas of the borehole radar system, there is obvious resonance, which is caused by the multiple reflections between the receiving antennas. However, when the fluid in the borehole is water and the relative permittivity of the sonde is low to a certain extent, the resonance disappears; that is, the generation of resonance requires a large relative permittivity material between the receiving antennas. When the influence of the sonde is considered, the resonance disappears because the relative permittivity of the sonde is low, which makes the propagation speed of the electromagnetic wave between the antennas accelerate and lose the conditions for resonance. In addition, the diameters of the sonde and the circular array of the receiving antennas can affect the received signal: the higher the diameter of the sonde and the higher the diameter of the circular array are, the better the differentiation of the received signal. The development of the research provides scientific guidance for the design and application of borehole radar in the future. [ABSTRACT FROM AUTHOR]

China is strongly dependent on railway transportation, but the frost heaving of the subgrade in cold regions has seriously affected the safety and comfort of trains. Moisture content is an essential parameter in the subgrade frost heave. Non-destructive and efficient geophysical methods have great potential in measuring the moisture content of railway subgrade. In this paper, we use the common mid-point (CMP) measurement of ground penetrating radar (GPR) to estimate the propagation velocity of electromagnetic waves in a subgrade application. We establish a synthetic model to simulate the railway subgrade structure. The synthetic CMP gathers acquired from shallow and thin layers are seriously disturbed by multiple waves and refraction waves, which make the routine velocity analysis unable to provide accurate velocities. Through the analysis of numerical simulation results, it is found that the primary reflection waves, multiple waves, and refraction waves are dominant in different offset ranges of CMP gather. Therefore, we propose a solution of the optimal gather at a certain range of offset dominated by the primary reflection wave to calculate the velocity spectrum and extract the accurate velocities for the subgrade model. The relative dielectric constants of the corresponding layers are calculated after the stacking velocities are converted into the interval velocities. Then, the moisture content is obtained by the Topp formula, which expresses the relationship between dielectric constant and moisture content. Finally, we apply the optimal gather scheme and the above interpretation process to the GPR data acquired at the railway site, and we form a long moisture content profile of the railway subgrade. Compared with the polarizability measured by the induced polarization (IP) method, it is found that the regions with high moisture content correspond to polarizability anomalies with different strengths. The comparison shows the reliability of GPR results to some extent. [ABSTRACT FROM AUTHOR]

The internal layers of ice sheets from ice-penetrating radar (IPR) investigation preserve critical information about the ice-flow field and englacial conditions. This paper presents a new detailed analysis of spatial distribution characteristics of internal layers and subglacial topography of the East Antarctic ice sheet (EAIS) from Zhongshan Station to Dome A. The radar data of 1244 km along a traverse between Zhongshan Station and Dome A of EAIS were collected during the 29th Chinese National Antarctic Research Expedition (CHINARE 29, 2012/2013). In this study, the Internal Layering Continuity Index (ILCI) and basal roughness were taken as indicators to provide an opportunity to evaluate the past internal environment and dynamics of the ice sheet. Except for the upstream of Lambert Glacier, the fold patterns of internal layers are basically similar to that of the bed topography. The relatively flat basal topography and the decrease of ILCI with increasing depth provide evidence for identifying previous rapid ice flow areas that are unavailable to satellites, especially in the upstream of Lambert Glacier. Continuous internal layers of Dome A, recording the spatial change of past ice accumulation and ice-flow history over 160 ka, almost extend to the bed, with high ILCI and high basal roughness of the corresponding bed topography. There are three kinds of basal roughness patterns along the traverse, that is, "low ξt low η", "low ξt high η", and "high ξt high η", where ξt represents the amplitude of the undulations, and quantifies the vertical variation of the bedrock, and η measures the frequency variation of fluctuations and the horizontal irregularity of the profile. The characteristics of internal layers and basal topography of the traverse between Zhongshan Station and Dome A provide new information for understanding the ancient ice-flow activity and the historical evolution of EAIS. [ABSTRACT FROM AUTHOR]

Full waveform inversion (FWI) can yield high resolution images and has been applied in Ground Penetrating Radar (GPR) for around 20 years. However, appropriate selection of the initial models is important in FWI because such an inversion is highly nonlinear. The conventional way to obtain the initial models for GPR FWI is ray-based tomogram inversion which suffers from several inherent shortcomings. In this paper, we develop a Laplace domain waveform inversion to obtain initial models for the time domain FWI. The gradient expression of the Laplace domain waveform inversion is deduced via the derivation of a logarithmic object function. Permittivity and conductivity are updated by using the conjugate gradient method. Using synthetic examples, we found that the value of the damping constant in the inversion cannot be too large or too small compared to the dominant frequency of the radar data. The synthetic examples demonstrate that the Laplace domain waveform inversion provide slightly better initial models for the time domain FWI than the ray-based inversion. Finally, we successfully applied the algorithm to one field data set, and the inverted results of the Laplace-based FWI show more details than that of the ray-based FWI. [ABSTRACT FROM AUTHOR]

Simple Summary: In recent years, the worldwide prohibition on antibiotics, including in China, has led to an increased incidence of acute enteritis in poultry, resulting in significant economic losses. Probiotic-fermented products, especially postbiotics, have exhibited promising probiotic effects, demonstrating potential for ameliorating acute enteritis. It has been reported that probiotic and postbiotics intervention can effectively treat acute enteritis. In reality, coconut water, an abundant local resource in Hainan, China, is frequently easy to be contaminated and consequently underutilized in industrial processes. In this study, Wenchang chicken was employed as an DSS-induced model of acute enteritis and then fed with coconut water fermented by probiotics. The results show that coconut water fermented by probiotics facilitates the recovery of production performance in afflicted chickens, improving serum immune and biochemical indexes, intestinal tissue structure, and the composition of the gut microbiota structure and metabolomics. This study provides theoretical insights for the development and utilization of new fermented feed resources known as postbiotics and provides a reference for the sustainable green development of the poultry breeding industry. In order to investigate the potential mechanisms of probiotic-fermented coconut water in treating enteritis, this study conducted a comprehensive analysis of the effects of probiotic intervention on the recovery from Dextran Sodium Sulfate-induced acute enteritis in Wenchang chicks. The analysis encompassed the assessment of growth performance, serum indicators, intestinal tissue structure, and metagenomic and metabolomic profiles of cecal contents in 60 Wenchang chicks subjected to intervention. This approach aimed to elucidate the impact of probiotic intervention on the recovery process from acute enteritis at both the genetic and metabolic levels in the avian model. The results revealed that intervention with Saccharomyces cerevisiae Y301 improved the growth rate of chicks. and intervention with Lactiplantibacillus plantarum MS2c regulated the glycerophospholipid metabolism pathway and reshaped the gut microbiota structure in modeling chicks with acute enteritis, reducing the abundance of potentially pathogenic bacteria from the Alistipes and increasing the abundance of potentially beneficial species from the Christensenellaceae. This intervention resulted in the production of specific gut metabolites, including Gentamicin C and polymyxin B2, recognized for their therapeutic effects on acute enteritis. The combined intervention of S. cerevisiae Y301 and L. plantarum MS2c not only enhanced growth performance but also mitigated intestinal wall damage and increased the abundance of gut metabolites such as gentamicin C and polymyxin B2, thereby mitigating symptoms of enteritis. Furthermore, this combined intervention reduced the levels of serum immune markers, including IL-10, IL-6, TNF-α, IFN-γ, and D-lactic acid, thus mitigating intestinal epithelial cell damage and promoting acute enteritis recovery. This study provides crucial insights into the mechanisms of action of probiotics and probiotic-fermented coconut water in acute enteritis recovery, offering new perspectives for sustainable farming practices for Wenchang chicken. [ABSTRACT FROM AUTHOR]

In the Arctic and Antarctic scientific expeditions, ice-penetrating radar is an effective method for studying the bedrock under the ice sheet and ice information within the ice sheet. Because of the low conductivity of ice and the relatively uniform composition of ice sheets in the polar regions, ice-penetrating radar is able to obtain deeper and more abundant data than other geophysical methods. However, it is still necessary to suppress the noise in radar data to obtain more accurate and plentiful effective information. In this paper, the entirely non-recursive Variational Mode Decomposition (VMD) is applied to the data noise reduction of ice-penetrating radar. VMD is a decomposition method of adaptive and quasi-orthogonal signals, which decomposes airborne radar data into multiple frequency-limited quasi-orthogonal Intrinsic Mode Functions (IMFs). The IMFs containing noise are then removed according to the information distribution in the IMF's components and the remaining IMFs are reconstructed. This paper employs this method to process the real ice-penetrating radar data, which effectively eliminates the interference noise in the data, improves the signal-to-noise ratio and obtains the clearer inner layer structure of ice. It is verified that the method can be applied to the noise reduction processing of polar ice-penetrating radar data very well, which provides a better basis for data interpretation. At last, we present fine ice structure within the ice sheet based on VMD denoised radar profile. [ABSTRACT FROM AUTHOR]

A borehole radar investigation was performed at the Sanzuodian reservoir, Chifeng, China to assess possible leakage paths located in the deep dam foundation. The key methodologies used include both single-hole reflection and cross-hole radar tomography, which make a high-resolution identification of the hydraulic connection paths between upstream and downstream sides possible. The leakage paths are characterized by direct wave loss due to high electromagnetic attenuation in the single-hole reflection profile and the nearly horizontal-banded low-velocity zone in the cross-hole velocity tomography due to possible large internal erosion. Meanwhile, some small structures inside the dam, including the core wall thickness changing point, the connecting point between asphalt and concrete walls, and the contacting interface between the dry and the water-saturated formations can be identified from the single-hole reflection profile clearly. Interpreted leakage paths are proven by the water flow measurement. Borehole radar is a useful high-resolution tool, suitable for deep leakage detection and evaluation. [ABSTRACT FROM AUTHOR]

Ground-penetrating radar (GPR) is an important tool for measuring soil water content (SWC) at the field scale. The amplitude analysis of the early time signal (ETS) of GPR may provide a rapid way to estimate SWC. By assuming a homogeneous medium, various studies have been conducted on the relationship between the amplitude of ETS and the topsoil layer's electromagnetic parameters (dielectric permittivity and conductivity) through numerical simulations, laboratory experiments, and field experiments. Soil is a typical inhomogeneous medium, and soil cultivation is a factor affecting its heterogeneity. In this context, we discuss the ability of the amplitude of ETS to estimate the water content of heterogeneous soil. First, we establish a multi-scale stochastic medium model with the inhomogeneous distribution of dielectric permittivity and conductivity and simulate the GPR response by the finite-difference time-domain (FDTD) method to observe the influence of medium heterogeneity on the GPR response. The heterogeneity of the soil models is evaluated by a geostatistical analysis described by two parameters, correlation length and variability. Then, we analyze the relationship between variability and the average envelope amplitude (AEA) of ETS. A strong soil heterogeneity increases the error of the AEA method in estimating SWC. Finally, the AEA method is used to estimate the SWC of two adjacent fields with different heterogeneities, which were caused by different cultivation methods. The results of the numerical simulation and field experiment indicate that the soil heterogeneity can have an impact on the estimation of SWC using EST, with an error lower than 3% within a depth range of 1/2 λ to λ (wavelength). This suggests that the EST of GPR can be applied to soil layers with relatively large lateral changes in water content. [ABSTRACT FROM AUTHOR]

Borehole radar is a powerful tool for detecting subsurface fractures. Fracture modeling and numerical simulation are essential means to study fracture detectability. In this article, we first propose a method to construct a single fracture model, which combines the Baecher disk model and random rough surface and includes features, such as roughness, pinch-out, and irregularity. As the precise description of the fracture raises the requirement for accuracy of the simulation algorithm, the 3-D conformal finite-difference time-domain (CFDTD) method is used in this work. Numerical simulations of a sphere and rough fractures show that the CFDTD has higher calculation accuracy than conventional FDTD. Then, we analyzed how the fractures with different roughness affect the electromagnetic wave response. It is found that as the fracture surface becomes rougher, the wave scattered by it becomes stronger, more fracture contour-related information is obtained, and the fracture morphology is recovered better. Combined with accurate fracture modeling and high-precision numerical simulation, the electromagnetic response characteristics of different forms of fractures are obtained, which provides a basis for the accurate detection and interpretation of fractures in the future. [ABSTRACT FROM AUTHOR]

Using pre-fermented coconut water brings about a high yield of bacterial cellulose (BC) from Komagataeibacter strains in food industry, but the production is unstable and even risky. Therefore, finding a controllable and high-yield production mode of BC is necessary. Our previous study has showed that Lactobacillus is one of the dominant genera in pre-fermented coconut water. Based on this, the effect of co-culture of K. nataicola and 17 coconut-sourced Lactobacillus spp. strains on the production of BC was investigated in this study. Results suggested that co-culture of K. nataicola and Lactobacillus spp. strains had varied effects on the production of BC. Co-culture of K. nataicola Q2 and L. fermentum SR can effectively improve the production of BC via affecting the formation of β-1,4-glucan chains and crystallization of microfibrils. Moreover, direct and indirect pathways were involved in promoting the formation of β-1,4-glucan chains in the co-culture system. The co-culture of K. nataicola Q2 and L. fermentum SR led to the production of BC membrane with higher crystallinity but lower thermal degradation, hardness, adhesiveness, and water holding capacity. This research provides a reference for realizing controllable increase of BC production and modification of BC. • Co-culture of K. nataicola and Lactobacillus strains variedly affected BC yield. • Co-culture of K. nataicola Q2 and L. fermentum SR enhanced BC yield by up to 4.5 folds. • Co-culture with L. fermentum SR promoted BC synthesis via two pathways. • Co-culture with L. fermentum SR increased BC crystallinity. • Co-culture with L. fermentum SR changed the texture profile and WHC of BC. [ABSTRACT FROM AUTHOR]

• Combined ultrasound and enzymatic treatment were used for the extraction of noni juice for the first time. • Ultrasonic process parameters for noni juice extraction were further optimized by response surface methodology. • Ultrasonication at 600 W for 10 min after enzymatic treatment (EZU) obtained the maximum juice yield. • EZU-treated noni juice achieved the highest bioactive ingredients content and antioxidant capacity. • EZU treatment is a good alternative to the individual method. In order to obtain noni juice with high yield and good quality, the effect of combined extraction technique of enzymatic treatment (EZ) and ultrasonication (US) on the overall quality of noni juice was investigated. Moreover, the extraction performance of the EZ-US combined extraction technique was compared with that of EZ-based extraction and the US-based extraction. Response surface methodology (RSM) was designed to optimize the parameters of ultrasonic treatment, by taking consideration of the extraction efficiency, quality parameters and bioactive ingredients of noni juice. The results indicated that combined ultrasonic and enzymatic treatment achieved a synergistic effect on promoting the quality of noni juice. The maximum juice yield of 67.95 % was obtained under ultrasonication for 10 min at 600 W after enzymatic treatment (EZU). In addition, EZU-treated juice exhibited the highest contents of total phenolic and flavonoid, which were 148.19 ± 2.53 mg gallic acid/100 mL and 47.19 ± 1.22 mg rutin/100 mL, respectively, thus contributing to better antioxidant activity. Moreover, the EZU treatment significantly reduced the particle size of noni juice, and improved its suspension stability and rheological properties. FTIR results indicated that the treatments did not bring major changes in the chemical structure and the functional groups of compounds in noni juice. Therefore, EZU treatment can be successfully applied to the extraction of noni juice with better nutritional properties and overall quality. [ABSTRACT FROM AUTHOR]

Pepper pericarp microbiota plays an important role in the pepper peeling process for the production of white pepper. We collected pepper samples at different peeling time points from Hainan Province, China, and used a metagenomic approach to identify changes in the pericarp microbiota based on functional gene analysis. UniFrac distance-based principal coordinates analysis revealed significant changes in the pericarp microbiota structure during peeling, which were attributed to increases in bacteria from the genera Selenomonas and Prevotella. We identified 28 core operational taxonomic units at each time point, mainly belonging to Selenomonas, Prevotella, Megasphaera, Anaerovibrio, and Clostridium genera. The results were confirmed by quantitative polymerase chain reaction. At the functional level, we observed significant increases in microbial features related to acetyl xylan esterase and pectinesterase for pericarp degradation during peeling. These findings offer a new insight into biodegradation for pepper peeling and will promote the development of the white pepper industry. [ABSTRACT FROM AUTHOR]

Bacterial cold water disease (BCWD) causes significant economic loss in salmonid aquaculture. Using microsatellite markers in a genome scan, we previously detected significant and suggestive QTL affecting phenotypic variation in survival following challenge with Flavobacterium psychrophilum, the causative agent of BCWD in rainbow trout. In this study, we performed selective genotyping of SNPs from restriction-site associated DNA (RAD) sequence data from two pedigreed families (2009070 and 2009196) to validate the major QTL from the previous work and to detect new QTL. The use of RAD SNPs in the genome scans increased the number of mapped markers from ~300 to ~5,000 per family. The significant QTL detected in the microsatellites scan on chromosome Omy8 in family 2009070 was validated explaining up to 58% of the phenotypic variance in that family, and in addition, a second QTL was also detected on Omy8. Two novel QTL on Omy11 and 14 were also detected, and the previously suggestive QTL on Omy1, 7 and 25 were also validated in family 2009070. In family 2009196, the microsatellite significant QTL on Omy6 and 12 were validated and a new QTL on Omy8 was detected, but none of the previously detected suggestive QTL were validated. The two Omy8 QTL from family 2009070 and the Omy12 QTL from family 2009196 were found to be co-localized with handling and confinement stress response QTL that our group has previously identified in a separate pedigreed family. With the currently available data we cannot determine if the co-localized QTL are the result of genes with pleiotropic effects or a mere physical proximity on the same chromosome segment. The genetic markers linked to BCWD resistance QTL were used to query the scaffolds of the rainbow trout reference genome assembly and the QTL-positive scaffold sequences were found to include 100 positional candidate genes. Several of the candidate genes located on or near the two Omy8 QTL detected in family 2009070 suggest potential linkages between stress response and the regulation of immune response in rainbow trout. [ABSTRACT FROM AUTHOR]

Selective breeding of animals for increased disease resistance is an effective strategy to reduce mortality in aquaculture. However, implementation of selective breeding programs is limited by an incomplete understanding of host resistance traits. We previously reported results of a rainbow trout selection program that demonstrated increased survival following challenge with Flavobacterium psychrophilum, the causative agent of bacterial cold water disease (BCWD). Mechanistic study of disease resistance identified a positive phenotypic correlation between post-challenge survival and spleen somatic-index (SI). Herein, we investigated the hypothesis of a genetic correlation between the two traits influenced by colocalizing QTL. We evaluated the inheritance and calculated the genetic correlation in five year-classes of odd- and even-year breeding lines. A total of 322 pedigreed families (n = 25,369 fish) were measured for disease resistance, and 251 families (n = 5,645 fish) were evaluated for SI. Spleen index was moderately heritable in both even-year (h2 = 0.56±0.18) and odd-year (h2 = 0.60±0.15) lines. A significant genetic correlation between SI and BCWD resistance was observed in the even-year line (rg = 0.45±0.20, P = 0.03) but not in the odd-year line (rg = 0.16±0.12, P = 0.19). Complex segregation analyses of the even-year line provided evidence of genes with major effect on SI, and a genome scan of a single family, 2008132, detected three significant QTL on chromosomes Omy19, 16 and 5, in addition to ten suggestive QTL. A separate chromosome scan for disease resistance in family 2008132 identified a significant BCWD QTL on Omy19 that was associated with time to death and percent survival. In family 2008132, Omy19 microsatellite alleles that associated with higher disease resistance also associated with increased spleen size raising the hypothesis that closely linked QTL contribute to the correlation between these traits. To our knowledge, this is the first estimation of spleen size heritability and evidence for genetic linkage with specific disease resistance in a teleost fish. [ABSTRACT FROM AUTHOR]

To improve our understanding of the organization and evolution of the wheat (Triticum aestivum) genome, we sequenced and annotated 13-Mb contigs (18.2 Mb) originating from different regions of its largest chromosome, 3B (1 Gb), and produced a 2x chromosome survey by shotgun Illumina/Solexa sequencing. All regions carried genes irrespective of their chromosomal location. However, gene distribution was not random, with 75% of them clustered into small islands containing three genes on average. A twofold increase of gene density was observed toward the telomeres likely due to high tandem and interchromosomal duplication events. A total of 3222 transposable elements were identified, including 800 new families. Most of them are complete but showed a highly nested structure spread over distances as large as 200 kb. A succession of amplification waves involving different transposable element families led to contrasted sequence compositions between the proximal and distal regions. Finally, with an estimate of 50,000 genes per diploid genome, our data suggest that wheat may have a higher gene number than other cereals. Indeed, comparisons with rice (Oryza sativa) and Brachypodium revealed that a high number of additional noncollinear genes are interspersed within a highly conserved ancestral grass gene backbone, supporting the idea of an accelerated evolution in the Triticeae lineages. [ABSTRACT FROM AUTHOR]

Nk-lysin (Nkl), an antimicrobial peptide (AMP) product of natural killer cells and cytotoxic T cells in mammals, has recently been characterized in a number of finfish species. In this study, we identified six genes with sequence homology to Nkl and characterized their patterns of mRNA expression and abundances in rainbow trout (Oncorhynchus mykiss). The cDNA sequences for the six Nkls encoded precursor peptides of 128–133 aa in length, and mature peptides of 109–111 aa in length. Genomic DNA of the nkl1-4 genes consisted of five exons and four introns, whereas the nkl-like a & b genes consisted of four exons and three introns. Chromosomal locations of these peptides show that nkl1 was located on chromosome arm 25q, whereas the other five nkl genes were clustered on chromosome arm 19q. Phylogenetic analysis revealed a conserved structure of Nkls among the teleosts and further protein sequence analyses suggests that all six nkl genes fall within the Nkl sub-family of the Saposin family of proteins. Patterns of tissue-specific mRNA expression were asymmetric among the six trout Nkl homologues, with nkl1 , nkl3 , and nkl-like a & b occurring in immune competent organs such as spleen, gill, intestine and kidney, as well as pineal gland, brain and oocytes. However, nkl2 and nkl4 , showed primary abundances in brain, pineal gland and oocyte tissues. Using mRNA sequencing, in whole-body pools of juvenile trout fry (1 g bw) exposed to Flavobacterium psychrophilum infection, we observed modest up-regulation (2–3 fold) of five (nkl 2–4 and nkl -like a & b) of the six nkl mRNAs over the five-day post-challenge time-course. However, no upregulation could be recorded in spleen tissue measured by qPCR in juvenile trout (270 g bw). Using mRNA sequencing again, mRNA abundances were determined in gill of juvenile trout (~57.7 g bw) exposed to various aquaculture stressors. The results indicated that all six nkl s (nkl1-4 and nkl-like a and nkl-like b) were downregulated when exposed to high temperature, and that nkl1 was significantly downregulated following salinity challenge. Overall, these newly characterized AMPs may contribute to host innate immunity as they are modulated following pathogen challenge and by physiological stressors. • Six homologues of the Nk-lysin proteins have been identified in rainbow trout. • Four Nkl (1-4) genes consisted of 5 exons and 4 introns, and the two Nkl-like a & b genes had 4 exons and 3 introns. • mRNA abundances for the six nkl genes were affected by challenge with F. psychrophilum and various aquaculture stressors. [ABSTRACT FROM AUTHOR]

The aim of this work was to compare the composition and physicochemical properties (SEM, XRD, solubility, swelling power, paste clarity, retrogradation, freeze–thaw stability, thermal property, and pasting property) of three Chinese yam (Dioscorea opposita Thunb.) starches (CYYS-1, CYYS-2, and CYYS-3) in Yunlong town, Haikou, Hainan Province, China. Our results show that all the CYYS gave a typical C-type X-ray diffraction pattern. The swelling power of CYYS varied from 10.79% to 30.34%, whereas solubility index was in the range of 7.84–4.55%. The freeze–thaw stability of each CYYS showed a contrary tendency with its amylose content. In addition, CYYS-3 showed the highest To (81.1 °C), Tp (84.8 °C), Tc (91.2 °C), and ΔH (14.1 J/g). The pasting temperature of CYYS-1 increased significantly with sucrose addition. NaCl could inhibit the swelling power of CYYS. There were significant decreases in pasting temperature and pasting time of CYYS when pH decreased. [ABSTRACT FROM AUTHOR]