A Comprehensive Assessment of Ultraviolet-Radiation-Induced Mutations in Flammulina filiformis Using Whole-Genome Resequencing.

Nucleotide substitutions have played an important role in molecular evolution, and understanding their dynamics would contribute to genetic studies. Related research with defined DNA sequences lasted for decades until whole-genome sequencing arose. UV radiation (UVR) can generate base changes and other genetic variations in a short period of time, so it would be more meaningful to explore mutations caused by UVR from a genomic perspective. The monokaryon enoki strain WT583 was selected as the experimental material in this study because it can spontaneously produce large amounts of oidia on PDA plates, and the monokaryons originating from oidia have the same genotype as their mother monokaryon. After exposure to UV radiation, 100 randomly selected mutants, with WT583 as the reference genome, were sent for genome sequencing. BWA, samtools, and GATK software were employed for SNP calling, and the R package CMplot was used to visualize the distribution of the SNPs on the contigs of the reference genome. Furthermore, a k-mer-based method was used to detect DNA fragment deletion. Moreover, the non-synonymous genes were functionally annotated. A total of 3707 single-base substitutions and 228 tandem mutations were analyzed. The immediate adjacent bases showed different effects on the mutation frequencies of adenine and cytosine. For adenine, the overall effects of the immediate 5'-side and 3'-side bases were T > A > C > G and A > T > G > C, respectively; for cytosine, the overall effects of the immediate 5'-side and 3'-side bases were T > C > A > G and C > T > A > G, respectively. Regarding tandem mutations, the mutation frequencies of double-transition, double-transversion, 3'-side transition, and 5'-side transition were 131, 8, 72, and 17, respectively. Transitions at the 3'-side with a high mutation frequency shared a common feature, where they held transversions at the 5'-side of A→T or T→A without covalent bond changes, suggesting that the sequence context of tandem motifs might be related to their mutation frequency. In total, 3707 mutation sites were non-randomly distributed on the contigs of the reference genome. In addition, pyrimidines at the 3'-side of adenine promoted its transversion frequency, and UVR generated DNA fragment deletions over 200 bp with a low frequency in the enoki genome. The functional annotation of the genes with non-synonymous mutation indicated that UVR could produce abundant mutations in a short period of time.

Early detection of acute ischemic stroke using Contrast-enhanced electrical impedance tomography perfusion.

A cerebral contrast-enhanced electrical impedance tomography perfusion method is developed for acute ischemic stroke during intravenous thrombolytic therapy. Several clinical contrast agents with stable impedance characteristics and high-conductivity contrast were screened experimentally as electrical impedance contrast agent candidates. The electrical impedance tomography perfusion method was tested on rabbits with focal cerebral infarction, and its capability for early detection was verified based on perfusion images. The experimental results showed that ioversol 350 performed significantly better as an electrical impedance contrast agent than other contrast agents (p < 0.01). Additionally, perfusion images of focal cerebral infarction in rabbits confirmed that the electrical impedance tomography perfusion method could accurately detect the location and area of different cerebral infarction lesions (p < 0.001). Therefore, the cerebral contrast-enhanced electrical impedance tomography perfusion method proposed herein combines traditional, dynamic continuous imaging with rapid detection and could be applied as an early, rapid-detection, auxiliary, bedside imaging method for patients after a suspected ischemic stroke in both prehospital and in-hospital settings.

Effective Electrical Impedance Tomography Based on Enhanced Encoder-Decoder Using Atrous Spatial Pyramid Pooling Module.

Electrical impedance tomography (EIT) is a noninvasive and radiation-free imaging method. As a "soft-field" imaging technique, in EIT, the target signal in the center of the measured field is frequently swamped by the target signal at the edge, which restricts its further application. To alleviate this problem, this study presents an enhanced encoder-decoder (EED) method with an atrous spatial pyramid pooling (ASPP) module. The proposed method enhances the ability to detect central weak targets by constructing an ASPP module that integrates multiscale information in the encoder. The multilevel semantic features are fused in the decoder to improve the boundary reconstruction accuracy of the center target. The average absolute error of the imaging results by the EED method reduced by 82.0%, 83.6%, and 36.5% in simulation experiments and 83.0%, 83.2%, and 36.1% in physical experiments compared with the errors of the damped least-squares algorithm, Kalman filtering method, and U-Net-based imaging method, respectively. The average structural similarity improved by 37.3%, 42.9%, and 3.6%, and 39.2%, 45.2%, and 3.8% in the simulation and physical experiments, respectively. The proposed method provides a practical and reliable means of extending the application of EIT by solving the problem of weak central target reconstruction under the effect of strong edge targets in EIT.

Real-time imaging of traumatic brain injury using magnetic induction tomography.

Objective. Early diagnosis of traumatic brain injury (TBI) is crucial for its prognosis; however, traditional computed tomography diagnostic methods rely on large medical devices with an associated lag time to receive results. Therefore, an imaging modality is needed that provides real-time monitoring, can easily be carried out to assess the extent of TBI damage, and thus guides treatment.Approach. In the present study, an improved magnetic induction tomography (MIT) data acquisition system was used to monitor TBI in an animal model and distinguish the injury level. A pneumatically controlled cortical impactor was used to strike the parietal lobe of anesthetized rabbits two or three times under the same parameter mode to establish two different rabbit models of TBI. The MIT data acquisition system was used to record data and continuously monitor the brain for one hour without intervention.Main results. A target with increased conductivity was clearly observed in the reconstructed image. The position was relatively fixed and accurate, and the average positioning error of the image was 0.013 72 m. The normalized mean reconstruction value of all images increased with time. The slope of the regression line of the normalized mean reconstruction value differed significantly between the two models (p< 0.0001).Significance. This indicates that in the animal model, the unique features of MIT may facilitate the early monitoring of TBI and distinguish different degrees of injuries, thereby reducing the risk and mortality of associated complications.

Fast Iterative Shrinkage-Thresholding Algorithm with Continuation for Brain Injury Monitoring Imaging Based on Electrical Impedance Tomography.

Electrical impedance tomography (EIT) is low-cost and noninvasive and has the potential for real-time imaging and bedside monitoring of brain injury. However, brain injury monitoring by EIT imaging suffers from image noise (IN) and resolution problems, causing blurred reconstructions. To address these problems, a least absolute shrinkage and selection operator model is built, and a fast iterative shrinkage-thresholding algorithm with continuation (FISTA-C) is proposed. Results of numerical simulations and head phantom experiments indicate that FISTA-C reduces IN by 63.2%, 47.2%, and 29.9% and 54.4%, 44.7%, and 22.7%, respectively, when compared with the damped least-squares algorithm, the split Bergman, and the FISTA algorithms. When the signal-to-noise ratio of the measurements is 80-50 dB, FISTA-C can reduce IN by 83.3%, 72.3%, and 68.7% on average when compared with the three algorithms, respectively. Both simulation and phantom experiments suggest that FISTA-C produces the best image resolution and can identify the two closest targets. Moreover, FISTA-C is more practical for clinical application because it does not require excessive parameter adjustments. This technology can provide better reconstruction performance and significantly outperforms the traditional algorithms in terms of IN and resolution and is expected to offer a general algorithm for brain injury monitoring imaging via EIT.

A pilot study of contrast-enhanced electrical impedance tomography for real-time imaging of cerebral perfusion.

Background: Real-time detection of cerebral blood perfusion can prevent adverse reactions, such as cerebral infarction and neuronal apoptosis. Our previous clinical trial have shown that the infusion of therapeutic fluid can significantly change the impedance distribution in the brain. However, whether this alteration implicates the cerebral blood perfusion remains unclear. To explore the feasibility of monitoring cerebral blood perfusion, the present pilot study established a novel cerebral contrast-enhanced electrical impedance tomography (C-EIT) technique. Materials and methods: Rabbits were randomly divided into two groups: the internal carotid artery non-occlusion (ICAN) and internal carotid artery occlusion (ICAO) groups. Both of groups were injected with glucose, an electrical impedance-enhanced contrast agent, through the right internal carotid artery under EIT monitoring. The C-EIT reconstruction images of the rabbits brain were analyzed according to the collected raw data. The paired and independent t-tests were used to analyze the remodeled impedance values of the left and right cerebral hemispheres within and between studied groups, respectively. Moreover, pathological examinations of brain were performed immediately after C-EIT monitoring. Results: According to the reconstructed images, the impedance value of the left cerebral hemisphere in the ICAN group did not change significantly, whereas the impedance value of the right cerebral hemisphere gradually increased, reaching a peak at approximately 10 s followed by gradually decreased. In the ICAO group, the impedance values of both cerebral hemispheres increased gradually and then began to decrease after reaching the peak value. According to the paired t-test, there was a significant difference (P < 0.001) in the remodeling impedance values between the left and right hemispheres in the ICAN group, and there was also a significant difference (P < 0.001) in the ICAO group. According to the independent t-test, there was a significant difference (P < 0.001) of the left hemispheres between the ICAN and ICAO groups. Conclusion: The cerebral C-EIT proposed in this pilot study can reflect cerebral blood perfusion. This method has potential in various applications in the brain in the future, including disease progression monitoring, collateral circulation judgment, tumor-specific detection, and brain function research.

Core-Shell ZIF67@ZIF8 Modified with Phytic Acid as an Effective Flame Retardant for Improving the Fire Safety of Epoxy Resins.

Despite many important industrial applications, epoxy resin (EP) suffers from high flammability and toxicity emission, extremely hampering their applications. To circumvent the problem, core-shell structured ZIF67@ZIF8 is successfully synthesized and further functionalized with phytic acid (PA) to obtain PA-ZIF67@ZIF8 hybrids. Then, it is used as an efficient flame retardant to reduce the fire risk of EP. The fire test results show a significant reduction in heat and smoke production. Compared with EP, incorporating 5.0 wt % PA-ZIF67@ZIF8 into EP, the peak heat release rate, total heat release, and peak carbon monoxide production are dramatically reduced by 42.2, 33.0, and 41.5%, respectively. Moreover, the EP/PA-ZIF67@ZIF8 composites achieve the UL-94 V-0 rating and the limiting oxygen index increases by 29.3%. These superior fire safety properties are mainly attributed to the excellent dispersion and the catalytic effect of metal oxide and phosphorus-containing compounds. This work provides an efficient strategy for preparing a promising ZIF-based flame retardant for enhancing flame retardancy and smoke toxicity suppression of EP.

Bioinformatics Analysis Combined With Experiments Predicts PUDP as a Potential Prognostic Biomarker for Hepatocellular Carcinoma Through Its Interaction With Tumor Microenvironment.

Hepatocellular carcinoma (HCC) is one of the deadliest tumors in the world and is notorious for poor prognosis. There is mounting evidence that pseudouridine performs key functions in the initiation and progression of several cancers. A previous study demonstrated that Pseudouridine 5'-phosphatase (PUDP) may be a novel prognostic biomarker in colorectal cancer. However, in the past, we have paid little attention to PUDP and we are still not clear about its function and role in cancer. In this study, a pan-cancer analysis of PUDP expression and prognosis was performed firstly using The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx) data and we found that PUDP may be a potential oncogene for HCC. Then the most potential upstream microRNA contributing to PUDP was identified as let-7c-5p through expression analysis, correlation analysis, and survival analysis. Subsequently, the result of single cell RNA sequencing (scRNA-seq) demonstrated that PUDP was significantly highly expressed on malignant cells. In addition, there are significantly positive correlations between PUDP and tumor immune cell infiltration, biomarkers of immune cells, and immune checkpoint expression, especially with tumor-promoting immune cells such as T cell regulatory (Treg), Myeloid-derived suppressor cell (MDSC), cancer-associated fibroblast (CAF). Moreover, we found the methylation level of three loci was positively correlated with PUDP expression and four loci were negatively correlated. 15 pairs of HCC and normal adjacent tissues from HCC patients who were treated at our center were used to verify the results of the bioinformatics analysis and the results of experiments are similar to the bioinformatics analysis. Our study demonstrated that HCC patients with high PUDP expression are less likely to benefit from immunotherapy, and in addition, we explored the relationship between PUDP and anticancer drugs. Finally, we explored the clinical relevance of PUDP, identified PUDP as an independent risk factor for HCC patients and constructed a prognostic model, used International Cancer Genome Consortium (ICGC) data to do external validation. Collectively, our study demonstrated that high expression of PUDP suggested a poor prognosis and low response to immunotherapy, providing new insight into the treatment and prognosis of HCC.

Adaptive threshold split Bregman algorithm based on magnetic induction tomography for brain injury monitoring imaging.

Objective. Traditional magnetic induction tomography (MIT) algorithms have problems in reconstruction, such as large area error (AE), blurred boundaries of reconstructed targets, and considerable image noise (IN). As the size and boundary of a lesion greatly affect the treatment plan, more accurate algorithms are necessary to meet clinical needs.Approach. In this study, adaptive threshold split Bregman (ATSB) is proposed for brain injury monitoring imaging in MIT. We established a 3D brain MIT simulation model with the actual anatomical structure and a phantom model and obtained the reconstructed images of single targets in different positions and multiple targets, using the Tikhonov, eigenvalue threshold regularisation (ETR), split Bregman (SB), and ATSB algorithms.Main results. Compared with the Tikhonov and ETR algorithms, the ATSB algorithm reduced the AE by 95% and the IN by 17% in a simulation and reduced the AE by 87% and IN by 6% in phantom experiments. Compared with the SB algorithm, the ATSB algorithm can reduce the difficulty of adjusting parameters and is easier to use in clinical practice. The simulation and phantom experiments results showed that the ATSB algorithm could reconstruct the target size more accurately and could distinguish multiple targets more effectively than the other three algorithms.Significance. The ATSB algorithm could improve the image quality of MIT and better meet the needs of clinical applications and is expected to promote brain injury monitoring imaging via MIT.

Libertellenone H, a Natural Pimarane Diterpenoid, Inhibits Thioredoxin System and Induces ROS-Mediated Apoptosis in Human Pancreatic Cancer Cells.

Libertellenone H (LH), a marine-derived pimarane diterpenoid isolated from arctic fungus Eutypella sp. D-1, has shown effective cytotoxicity on a range of cancer cells. The present study is to explore the anticancer effect of LH on human pancreatic cancer cells and to investigate the intracellular molecular target and underlying mechanism. As shown, LH exhibited anticancer activity in human pancreatic cancer cells by promoting cell apoptosis. Mechanistic studies suggested that LH-induced reactive oxygen species (ROS) accumulation was responsible for apoptosis as antioxidant N-acetylcysteine (NAC) and antioxidant enzyme superoxide dismutase (SOD) antagonized the inhibitory effect of LH. Zymologic testing demonstrated that LH inhibited Trx system but had little effect on the glutathione reductase and glutaredoxin. Mass spectrometry (MS) analysis revealed that the mechanism of action was based on the direct conjugation of LH to the Cys32/Cys35 residue of Trx1 and Sec498 of TrxR, leading to a decrease in the cellular level of glutathione (GSH) and activation of downstream ASK1/JNK signaling pathway. Taken together, our findings revealed LH was a marine derived inhibitor of Trx system and an anticancer candidate.

Optimization of ultrasonic-assisted extraction of polysaccharides and triterpenoids from the medicinal mushroom Ganoderma lucidum and evaluation of their in vitro antioxidant capacities.

Ganoderma lucidum (Fr.) Krast, commonly known as "Lingzhi" in Chinese, is a medicinal mushroom that is rich in biologically active substances. Polysaccharides and triterpenoids are the two major components responsible for the bioactivity of this fungus. In the present study, the ultrasonic-assisted co-extraction (UACE) of polysaccharides and triterpenoids from G. lucidum was optimized using response surface methodology with a desirability function, with the equal importance for the two components. Following single factor experiments, the optimal conditions were determine as ultrasonic power of 210 W, extraction temperature of 80C, ratio of liquid to solid of 50 mL/g, and 100 min extraction time, using aqueous ethanol (50%, v/v) as the extracting solvent. Under the optimal conditions, the extraction yields of polysaccharides and triterpenoids reached 0.63% and 0.38%, respectively. On the basis of the scavenging capacity of 2,2-diphenyl-1-picrylhydrazyl and evaluation of reducing power, the antioxidant capacities of the polysaccharides obtained by optimal UACE process were higher than those of polysaccharides extracted using traditional hot water extraction, whereas the triterpenoid-rich extracts showed antioxidant activities similar to those obtained using the ethanol maceration method. The present study is the first report on the simultaneous extraction of polysaccharides and triterpenoids from G. lucidum. The developed UACE process could be useful in preparation of a polysaccharide- and triterpenoid-rich ingredient that holds great promise for application in the Ganoderma industry.

The complete chloroplast genome of Fraxinus hupehensis and phylogenic analysis of Lamiales.

Fraxinus hupehensis is a national rare and Endangered tree in the Oleaceae family, that has high commercial value owing to its slow growth, interlaced roots, intricate tree shape, and easy to shape. Here, we determined the complete chloroplast (cp) genome sequence for F. hupehensis using genome skimming sequencing. The cp genome was 155,698 bp and consisted of a large single copy (LSC) region (86,498 bp), a small single copy (SSC) region (17,803 bp) and two inverted repeats (IRs) (25,694 bp). It encodes 131 genes, including 88 protein-coding genes, 8 rRNAs and 35 tRNAs. Phylogenetic analysis indicates that F. hupehensis was relatively closely related to F. chinensis compared to other species in the Oleaceae family.

Optimization of submerged culture conditions involving a developed fine powder solid seed for exopolysaccharide production by the medicinal mushroom Ganoderma lucidum.

To facilitate Ganoderma lucidum submerged cultivation and achieve high productivity, four fine powder solid substrates incorporated with different nitrogen-rich supplements were utilized to grow the fungus and as solid seed for its submerged culture. Of the four solid seeds, the soybean meal solid seed gave the highest biomass (10.73 g/L) and exopolysaccharide (EPS) (1.22 g/L), higher than those (8.36 g/L biomass and 0.44 g/L EPS) obtained with mycelial liquid seed. The optimal level of soybean meal supplementation was 20% (w/w) for production of the solid seed. Following single factor experiments, levels of three selected process variables were optimized as: the moisture content of solid seed, 70%; inoculum size, 0.8 g/flask; and rotary speed, 160 rpm. These conditions were validated experimentally with improved EPS yield of 1.33 g/L. The developed solid seed can be conveniently used for G. lucidum submerged culture with improved EPS productivity.

Development of a Novel Spawn (Block Spawn) of an Edible Mushroom, Pleurotus ostreatus, in Liquid Culture and its Cultivation Evaluation.

Mushroom cultivation has gained increased attention in recent years. Currently, only four types of spawn, including sawdust spawn, grain spawn, liquid spawn, and stick spawn, are commonly available for mushroom cultivation. This limited spawn diversity has led to difficulty in selecting suitable inoculum materials in some cultivation. In this study, three small blocks of lignocellulosic agro-wastes and one block of a synthetic matrix were prepared as support for growing Pleurotus ostreatus in liquid medium. Mycelium-adsorbed blocks were then evaluated for their potential as block spawn for fructification. Our results indicated that the edible fungus was adsorbed and abundantly grew internally and externally on loofah sponge and synthetic polyurethane foam (PUF) supports and also has the ability to attach and grow on the surface of sugarcane bagasse and corncob supports. The mycelia of P. ostreatus adhered on corncob exhibited the highest metabolic activity, while those on the PUF showed the least activity. Mycelial extension rates of block spawns made of agro-waste materials were comparable to that of sawdust spawn, but the block spawn of PUF showed a significantly lower rate. No significant differences in cropping time and yield were observed among cultivations between experimental block spawns and sawdust spawns. Moreover, the corncob block spawn maintained its fruiting potential during an examined period of 6-month storage. The developed block spawn could be practically applied in mushroom cultivation.

Hyperproduction of exopolysaccharides by submerged mycelial culture of Ganoderma lucidum using a solid seed grown in fine-powder of wheat bran and in vitro evaluation of the antioxidant activity of the exopolysaccharides produced.

To facilitate Ganoderma lucidum submerged culture and obtain high productivity, a fine powder of wheat bran was used to grow the fungus for solid-state fermentation and as solid seed for its submerged cultures. The results indicated that the optimal inoculum size was low, being 0.75 g in 250 mL-sized flasks containing 80 mL medium. The maximal exopolysaccharide concentration and biomass produced was 0.74 and 14.71 g/L, respectively, which is considerably higher than that obtained with the commonly used mycelial pellet liquid seed (0.47 and 8.56 g/L, respectively). The EPS and biomass productivity of the solid seed cultures decreased only slightly, even after a 6-month storage period. EPS produced showed higher antioxidant activity compared with that produced in the liquid seed cultures. The developed solid seed can serve as a ready-to-use inoculum for long-term use in G. lucidum submerged culture for the hyperproduction of highly bioactive EPS and biomass.

Construction of multifunctional porous silica nanocarriers for pH/enzyme-responsive drug release.

pH/enzyme-responsive nanocarriers based on porous silica (pSiO2) nanospheres (NSs) were developed for controlled release of drug. The pSiO2 NSs present uniform spheres and have an average diameter of 100nm. The pSiO2 NSs with high specific surface area (835m2·g-1) and the pore volume (1.24cm3·g-1) are suitable for drug loading and the loading capacity reaches to 29% for amoxicillin (AMX) model drug. In this system, protocatechuic acid (PCA) and L-glutamic acid (Glu) as linkers were grafting onto the surface of pSiO2 NSs to conjugate the capping lids. Acid-decomposable ZnO quantum dots (QDs) were introduced to block the partial pores of pSiO2 via amido bonds, which could act as gates and fluorescence probes. To minimize the premature release, hyaluronic acid (HA) was further coating on the outer surface of pSiO2, which would be degraded by over-expressed hyaluronidase (Hyal-1) in the tumor microenvironment. The controlled release of the drug from the ZnO/HA-gated delivery system was realized by the acidic dissolution of ZnO QDs and enzymatic hydrolysis of HA. The obtained ZnO/HA-gated pSiO2 delivery system would achieve minimized premature release and responsive release under a physiological environment.

Inhibitors of Protein Tyrosine Phosphatase 1B from Marine Natural Products.

The ocean is a capacious area with the most abundant biological resources on the earth. The particularity of the marine ecological environment (high pressure, high salt, and hypoxia) makes the marine species survival competition fiercely, forcing many marine organisms in the process of life to produce a great deal of secondary metabolites with special structures and biological activities. In this article, 118 natural products which were isolated from four kinds of marine organisms, sponges, algae, soft corals and fungus, showing PTP1B inhibitory activity were summarized from 2010 to 2016, which may become the leading compounds towards treating Diabetes mellitus (DM). What's more, we briefly summarized the structure-activity relationship of PTP1B inhibitors.

Investigating the Effect of Tissue Size on Mycelial Growth of Seven Mushroom Species by Using a Novel Device for Precise Tissue Isolation.

Tissue isolation from mushrooms is frequently practiced by both researchers and growers to isolate new and improved strains. In the present study, we designed a simple and convenient device for precise tissue isolation and therefore investigated the effect of tissue size on mycelial growth of seven mushroom species. The developed device consists of a cutting needle and a transfer needle. The cutting needle was used to obtain circular tissue plugs having a height up to 3 mm and variable diameters (2-5 mm) from mushroom fruit bodies. The transfer needle was a stainless steel round rod (1.5 mm in diameter) with a blade-like end. It can be used for collecting mushroom tissue when the cutting needle fails to extract it. With the aid of these devices, precise tissue isolation was achieved. Plate cultures demonstrated that tissue size had little effect on mycelium extension for Lentinula edodes (the winter shiitake), Hypsizygus marmoreus, and Agrocybe aegerita, but influenced the aerobic mycelium density. For Pleurotus ostreatus, Pleurotus eryngii, and Volvariella volvacea, large tissue plugs produced faster mycelial growth and higher aerobic mycelium density compared with small ones. On the contrary, small plugs from the tissue of the flower shiitake and Agaricus bisporus favored mycelial growth. The present study revealed that the preferable tissue size for mycelial growth varies among mushroom species, and the developed device is expected to greatly facilitate the isolation of new and improved mushroom strains.

Isolation and characterization of microsatellite markers for Jasminum sambac (Oleaceae) using Illumina shotgun sequencing.

PREMISE OF THE STUDY: Microsatellite markers of Jasminum sambac (Oleaceae) were isolated to investigate wild germplasm resources and provide markers for breeding. METHODS AND RESULTS: Illumina sequencing was used to isolate microsatellite markers from the transcriptome of J. sambac. A total of 1322 microsatellites were identified from 49,772 assembled unigenes. One hundred primer pairs were randomly selected to verify primer amplification efficiency. Out of these tested primer pairs, 31 were successfully amplified: 18 primer pairs yielded a single allele, seven exhibited fixed heterozygosity with two alleles, and only six displayed polymorphisms. CONCLUSIONS: This study obtained the first set of microsatellite markers for J. sambac, which will be helpful for the assessment of wild germplasm resources and the development of molecular marker-assisted breeding.

Brain extraction from cerebral MRI volume using a hybrid level set based active contour neighborhood model.

BACKGROUND: The extraction of brain tissue from cerebral MRI volume is an important pre-procedure for neuroimage analyses. The authors have developed an accurate and robust brain extraction method using a hybrid level set based active contour neighborhood model. METHODS: The method uses a nonlinear speed function in the hybrid level set model to eliminate boundary leakage. When using the new hybrid level set model an active contour neighborhood model is applied iteratively in the neighborhood of brain boundary. A slice by slice contour initial method is proposed to obtain the neighborhood of the brain boundary. The method was applied to the internet brain MRI data provided by the Internet Brain Segmentation Repository (IBSR). RESULTS: In testing, a mean Dice similarity coefficient of 0.95±0.02 and a mean Hausdorff distance of 12.4±4.5 were obtained when performing our method across the IBSR data set (18 × 1.5 mm scans). The results obtained using our method were very similar to those produced using manual segmentation and achieved the smallest mean Hausdorff distance on the IBSR data. CONCLUSIONS: An automatic method of brain extraction from cerebral MRI volume was achieved and produced competitively accurate results.