Comparative analysis of microbial community structure in the ponds with different aquaculture model and fish by high-throughput sequencing.

The pond has a complex microbial ecosystem, including microorganisms in water and sediment, which plays an important role in the health of fish and water quality. The microbial community structure in the ponds can be easily affected by many factors. However, not much is known about the role of different aquaculture model and fish on the microbial community structure in ponds. The purpose of the study was to investigate the microbial diversity and composition of the ponds with different aquaculture model and fish by high-throughput sequencing. A total of 3835072 valid sequences were achieved from 60 samples. Additionally, 2064 and 1917 core OTUs were observed in water and sediment samples, respectively. Our results suggested that sediment samples have a higher abundance and diversity of microbial community than water samples. In all the samples, the four most dominant phyla were Proteobacteria, Cyanobacteria, Actinomycetes and Bacteroides. At the genus level, hgcI_clade and CL500-29_marine_group were the dominant bacteria shared by the water samples and sediment samples. In addition, more bacteria related to eutrophication were found in the group of BF, BC and HSB, which suggested that these ponds may have been eutrophicated. In conclusion, the present study revealed the differences in the structure and diversity of microbial communities in ponds with different aquaculture model and fish. Furthermore, changes in typical bacteria of the ponds contribute to detect water quality and prevent water eutrophication.

A vascular image registration method based on network structure and circuit simulation.

BACKGROUND: Image registration is an important research topic in the field of image processing. Applying image registration to vascular image allows multiple images to be strengthened and fused, which has practical value in disease detection, clinical assisted therapy, etc. However, it is hard to register vascular structures with high noise and large difference in an efficient and effective method. RESULTS: Different from common image registration methods based on area or features, which were sensitive to distortion and uncertainty in vascular structure, we proposed a novel registration method based on network structure and circuit simulation. Vessel images were transformed to graph networks and segmented to branches to reduce the calculation complexity. Weighted graph networks were then converted to circuits, in which node voltages of the circuit reflecting the vessel structures were used for node registration. The experiments in the two-dimensional and three-dimensional simulation and clinical image sets showed the success of our proposed method in registration. CONCLUSIONS: The proposed vascular image registration method based on network structure and circuit simulation is stable, fault tolerant and efficient, which is a useful complement to the current mainstream image registration methods.

Noninvasive IDH1 mutation estimation based on a quantitative radiomics approach for grade II glioma.

OBJECTIVE: The status of isocitrate dehydrogenase 1 (IDH1) is highly correlated with the development, treatment and prognosis of glioma. We explored a noninvasive method to reveal IDH1 status by using a quantitative radiomics approach for grade II glioma. METHODS: A primary cohort consisting of 110 patients pathologically diagnosed with grade II glioma was retrospectively studied. The radiomics method developed in this paper includes image segmentation, high-throughput feature extraction, radiomics sequencing, feature selection and classification. Using the leave-one-out cross-validation (LOOCV) method, the classification result was compared with the real IDH1 situation from Sanger sequencing. Another independent validation cohort containing 30 patients was utilised to further test the method. RESULTS: A total of 671 high-throughput features were extracted and quantized. 110 features were selected by improved genetic algorithm. In LOOCV, the noninvasive IDH1 status estimation based on the proposed approach presented an estimation accuracy of 0.80, sensitivity of 0.83 and specificity of 0.74. Area under the receiver operating characteristic curve reached 0.86. Further validation on the independent cohort of 30 patients produced similar results. CONCLUSIONS: Radiomics is a potentially useful approach for estimating IDH1 mutation status noninvasively using conventional T2-FLAIR MRI images. The estimation accuracy could potentially be improved by using multiple imaging modalities. KEY POINTS: • Noninvasive IDH1 status estimation can be obtained with a radiomics approach. • Automatic and quantitative processes were established for noninvasive biomarker estimation. • High-throughput MRI features are highly correlated to IDH1 states. • Area under the ROC curve of the proposed estimation method reached 0.86.

Anatomic mapping of molecular subtypes in diffuse glioma.

BACKGROUND: Tumor location served as an important prognostic factor in glioma patients was considered to postulate molecular features according to cell origin theory. However, anatomic distribution of unique molecular subtypes was not widely investigated. The relationship between molecular phenotype and histological subgroup were also vague based on tumor location. Our group focuses on the study of glioma anatomic location of distinctive molecular subgroups and histology subtypes, and explores the possibility of their consistency based on clinical background. METHODS: We retrospectively reviewed 143 cases with both molecular information (IDH1/TERT/1p19q) and MRI images diagnosed as cerebral diffuse gliomas. The anatomic distribution was analyzed between distinctive molecular subgroups and its relationship with histological subtypes. The influence of tumor location, molecular stratification and histology diagnosis on survival outcome was investigated as well. RESULTS: Anatomic locations of cerebral diffuse glioma indicate varied clinical outcome. Based on that, it can be stratified into five principal molecular subgroups according to IDH1/TERT/1p19q status. Triple-positive (IDH1 and TERT mutation with 1p19q codeletion) glioma tended to be oligodendroglioma present with much better clinical outcome compared to TERT mutation only group who is glioblastoma inclined (median overall survival 39 months VS 18 months). Five molecular subgroups were demonstrated with distinctive locational distribution. This kind of anatomic feature is consistent with its corresponding histological subtypes. DISCUSSION: Each molecular subgroup in glioma has unique anatomic location which indicates distinctive clinical outcome. Molecular diagnosis can be served as perfect complementary tool for the precise diagnosis. Integration of histomolecular diagnosis will be much more helpful in routine clinical practice in the future.

Anatomical location differences between mutated and wild-type isocitrate dehydrogenase 1 in low-grade gliomas.

Anatomical location of gliomas has been considered as a factor implicating the contributions of a specific precursor cells during the tumor growth. Isocitrate dehydrogenase 1 (IDH1) is a pathognomonic biomarker with a significant impact on the development of gliomas and remarkable prognostic effect. The correlation between anatomical location of tumor and IDH1 states for low-grade gliomas was analyzed quantitatively in this study. Ninety-two patients diagnosed of low-grade glioma pathologically were recruited in this study, including 65 patients with IDH1-mutated glioma and 27 patients with wide-type IDH1. A convolutional neural network was designed to segment the tumor from three-dimensional magnetic resonance imaging images. Voxel-based lesion symptom mapping was then employed to study the tumor location distribution differences between gliomas with mutated and wild-type IDH1. In order to characterize the location differences quantitatively, the Automated Anatomical Labeling Atlas was used to partition the standard brain atlas into 116 anatomical volumes of interests (AVOIs). The percentages of tumors with different IDH1 states in 116 AVOIs were calculated and compared. Support vector machine and AdaBoost algorithms were used to estimate the IDH1 status based on the 116 location features of each patient. Experimental results proved that the quantitative tumor location measurement could be a very important group of imaging features in biomarker estimation based on radiomics analysis of glioma.

[Image Fusion of Dyna CT and Digital Subtraction Angiography for Arteriovenous Malformations].

Both Dyna CT,a rotational faultage reconstructed technique,and digital subtraction angiography(DSA)play important roles in the diagnosis and treatment of arteriovenous malformations(AVM).Three-dimensional Dyna CT can provide the spatial information of AVM nidus,while two-dimensional DSA can provide the time information for distinguishing arteries and veins.To illustrate the location relationship of the nidus,arteries and veins at the same time,these two imaging modalities need to be fused.In this paper,a two-dimensional to three-dimensional back projection and growing method is proposed,which realizes the image fusion of two-dimensional DSA and threedimensional Dyna CT and achieves the differentiation of arteries and veins in Dyna CT.The experimental results showed that the fusion image could present both the position information of AVM nidus and the dynamic information of the blood vessels.Therefore,the proposed method can help surgeons locate the AVM abnormality and make operation plan more accurately.

[Design of the Mobile ECG Monitoring System Based on Android 4.3].

To monitor and record Electrocardiograph (ECG) signals for 24 hours, a mobile ECG monitoring system is designed based on Android 4.3. In this system, domestic indigenous E9622A is used to acquire ECG signals and TI CC2541 is adopted to communicate with mobile phones. The program is implemented on the Android platform to display and process ECG signals. The whole system is integrated on a 2 cm x 2 cm PCB. From experiments, it is shown that ECG signals can be obtained effectively when this system is worn, and clear ECG waveforms and parameters can be shown on the phones. With this system, arrhythmia can be diagnosed preliminarily. It is also shown that the system is low-power, low-cost, flexible and portable.

Characterization and phylogenetic analysis of the complete mitochondrial genome of sun loach (Yasuhikotakia eos).

The complete mitochondrial genome of the sun loach (Yasuhikotakia eos) was determined based on Illumina data in this study. The result showed that the closed double-stranded circular mitogenome was 16,738 bp in total length (GenBank accession number: MT800510) with 58.41% AT. The mitochondrial DNA consisted of 13 protein-coding genes (PGCs), 22 transfer RNA (tRNA) genes, 2 ribosomal (rRNA) genes, and 1 non-coding control region. Phylogenetic analysis suggested that Y. eos was most closely related to its congener Y. modesta. This work provides molecular information for further research on species identification and evolutionary relationships.

Sustainable farming practices of the Chinese mitten crab (Eriocheir sinensis) around Hongze Lake, lower Yangtze River Basin, China.

Results of a survey of 156 Chinese mitten crab (Eriocheir sinensis) grow-out farms around Hongze Lake (118.48-118.72°E; 33.36-33.38°N) are reported. Area farmed has remained relatively unchanged but production (59 932 t in 2012) increased steadily over the last 7 years, indicative of the viability and sustainability of the farming system that has gradually replaced intensive Chinese major carp polyculture around Hongze Lake. Results showed that production range was 135-2400 kg ha(-1) cycle(-1) (mean 1144 ± 34). Crab yields correlated linearly to stocking density and conformed to a normal distribution curve, with 66.7 % of farms yielding 900 kg ha(-1) cycle(-1) or more. Yield was negatively correlated to pond size and capture size (p < 0.01), and farms with macrophyte coverage rate lower than 30 % of water surface were significantly (p < 0.05) lower than those exceeding 30 %.