A Coarse-to-Fine Fusion Network for Small Liver Tumor Detection and Segmentation: A Real-World Study.

Liver tumor semantic segmentation is a crucial task in medical image analysis that requires multiple MRI modalities. This paper proposes a novel coarse-to-fine fusion segmentation approach to detect and segment small liver tumors of various sizes. To enhance the segmentation accuracy of small liver tumors, the method incorporates a detection module and a CSR (convolution-SE-residual) module, which includes a convolution block, an SE (squeeze and excitation) module, and a residual module for fine segmentation. The proposed method demonstrates superior performance compared to conventional single-stage end-to-end networks. A private liver MRI dataset comprising 218 patients with a total of 3605 tumors, including 3273 tumors smaller than 3.0 cm, were collected for the proposed method. There are five types of liver tumors identified in this dataset: hepatocellular carcinoma (HCC); metastases of the liver; cholangiocarcinoma (ICC); hepatic cyst; and liver hemangioma. The results indicate that the proposed method outperforms the single segmentation networks 3D UNet and nnU-Net as well as the fusion networks of 3D UNet and nnU-Net with nnDetection. The proposed architecture was evaluated on a test set of 44 images, with an average Dice similarity coefficient (DSC) and recall of 86.9% and 86.7%, respectively, which is a 1% improvement compared to the comparison method. More importantly, compared to existing methods, our proposed approach demonstrates state-of-the-art performance in segmenting small objects with sizes smaller than 10 mm, achieving a Dice score of 85.3% and a malignancy detection rate of 87.5%.

Protocol for Brain Magnetic Resonance Imaging and Extraction of Imaging-Derived Phenotypes from the China Phenobank Project.

Imaging-derived phenotypes (IDPs) have been increasingly used in population-based cohort studies in recent years. As widely reported, magnetic resonance imaging (MRI) is an important imaging modality for assessing the anatomical structure and function of the brain with high resolution and excellent soft-tissue contrast. The purpose of this article was to describe the imaging protocol of the brain MRI in the China Phenobank Project (CHPP). Each participant underwent a 30-min brain MRI scan as part of a 2-h whole-body imaging protocol in CHPP. The brain imaging sequences included T1-magnetization that prepared rapid gradient echo, T2 fluid-attenuated inversion-recovery, magnetic resonance angiography, diffusion MRI, and resting-state functional MRI. The detailed descriptions of image acquisition, interpretation, and post-processing were provided in this article. The measured IDPs included volumes of brain subregions, cerebral vessel geometrical parameters, microstructural tracts, and function connectivity metrics.

The complete mitochondrial genome of the Orange Hairstreak Japonica lutea (Lepidoptera: Lycaenidae: Theclinae).

The complete mitochondrial genome of Japonica lutea is 15,225 bp in length, containing 37 typical insect genes: 13 protein-coding genes, 22 tRNA genes, 2 ribosomal RNA genes and a non-coding AT-rich region. All the 13 PCGs are initiated with ATN, except for COI gene which is started by CGA. Nine PCGs use the complete termination codon (TAN), whereas the COI, COII, ND4 and ND5 genes end with single nucleotide T. In total, 131 bp intergenic spacers and 31 bp overlapping sequences are interspersed throughout the whole genome. The two rRNA genes (lrRNA and srRNA) are 1327 bp and 770 bp in size, with their AT contents of 87.8% and 85.5%, respectively. All tRNAs display typical secondary cloverleaf structures except for tRNASer(AGN) which loses the DHU arm. The 401 bp long AT-rich region contains several features characteristic of the lepidopterans, such as the ATAGA motif followed by a 19 bp poly-T stretch, a microsatellite-like (AT)7 element preceded by the ATTTA motif and a 9 bp poly-A stretch.

The complete mitochondrial genome of Parnassius imperator (Lepidoptera: Papilionidae: Parnassiinae).

The complete mitochondrial genome (mitogenome) of Parnassius imperator (Lepidoptera: Parnassiinae) is a circular molecule of 15,424 bp in length, containing 37 typical insect mitochondrial genes and one non-coding A + T-rich region. Its gene order and arrangement are identical to the common type found in most lepidopteran mitogenomes. All protein-coding genes (PCGs) start with a typical ATN initiation codon, except for the cox1, which is initiated by the CGA codon as observed in other lepidopteran species. Some PCGs use standard TAA, while others use TAG (nad1) or incomplete codon T (cox1 and cox2), as their termination codons. 15 intergenic spacers (175 bp in total) and 10 overlapping sequences (29 bp in total) are dispersed throughout the whole genome. The 491 bp long A+ T-rich region contains some conserved structures similar to those found in other lepidopteran mitogenomes, such as the motif ATAGA followed by an 18-bp poly-T stretch, a microsatellite-like (AT)6 element preceded by the ATTTA motif. In addition, a 36 bp sequence stretch potential to form stem-loop structures is also found in the A+ T-rich region.

[Preparation and identification of anti-follicle-stimulating hormone receptor nanobodies].

OBJECTIVE: To prepare camel derived nanobodies which specifically bind to follicle-stimulating hormone receptor (FSHR). METHODS: The FSHR gene fragment (fshr234) was expressed in E.coli as antigen for affinity screening against VHH phage display library constructed from Xinjiang Bactrian camel. After confirmed by DNA sequencing, the vhh gene fragments of interest were subcloned into pET30a expression vector, and then were used to transform E.coli BL21(DE3). After IPTG induction, 6×His and c-Myc tagged fusion nanobodies were expressed. The nanobodies were purified by Ni-ion affinity chromatography. The binding specificity of nanobodies with His-FSHR234 was determined by ELISA. RESULTS: By enrichment screening with the antigen His-FSHR234, the 28 clones showed VHH sequence identities in DNA sequencing from 40 randomly selected binding clones. The 4 clones were subcloned into pET30a vector and confirmed as expected size of inserts by PCR and endonuclease digestion. The 4 expressed and affinity purified recombinant nanobodies namely VHHFSHR;-06, VHHFSHR;-25, VHHFSHR;-30 and VHHFSHR;-50 showed single band at Mr; 31 000, 26 000, 25 000 and 26 000 on SDS-PAGE, respectively. ELISA results showed that 4 nanobodies could bind to FSHR234 specifically, in which VHHFSHR;-06 showed the highest antigen binding activity. CONCLUSION: By screening camel VHH phage display library with His-FSHR234 antigen, one nanobody, VHHFSHR;-06 with relatively high antigen binding activity has been produced and identified.

[Preparation and property study of the recombinant Camel anti-SpaA-N single domain antibodies].

AIM: In order to obtain single domain antibody against surface protective antigen A (SpaA)of Erysipelothrix rhusiopathiae. METHODS: The SpaA-N recombinant protein was used to screen binders from Bactrian camel VHH phage display library. After sequencing, the interested VHH gene fragments were subcloned into pET-30a vector to overexpress the protein in E.coli BL21. The binding specificity of the recombinant VHH with SpaA-N was determined by Western blotting. The thermal stability of single-domain antibody was evaluated by ELISA. RESULTS: By enrichment of screening, 2 clones were selected. Recombinant single domain antibodies purified by Ni-ion affinity chromatography showed a single band at M(r); 29 000, 23 000 on SDS-PAGE. ELISA results showed that VHH can bind its antigen specifically. After thermal denaturation, VHH can restore the antigen binding ability after refolding. Western blotting results showed that the recombinant VHH specific bind surface protective antigen of Erysipelothrix rhusiopathiae at M(r); 66 000. Two VHH single domain antibodies with high thermal stability and good antigen binding specificity were identified by screening Bactrian camel VHH phage display library. CONCLUSION: Two single domain antibodies that specifically aggulated SpaA-N is obtained, which provide the basis for further study in the immune role of single domain antibody against Erysipelothrix rhusiopathiae infection.

[Analysis on data from the clinical acute viral encephalitis surveillance system in three prefectures in Shaanxi during 2005 - 2006].

OBJECTIVE: To describe the epidemiological features of viral encephalitis and burden of Japanese encephalitis (JE), and to identify potential strategies for effective JE control measures, using data from the Viral Encephalitis Surveillance Program (VESP) launched in Ankang, Baoji, and Weinan prefectures, Shaanxi province. METHODS: Data was gathered from sentinel hospitals reporting system on all the viral encephalitis (VE) cases identified between June 2005 and May 2007. County Center for Disease Control and Prevention (CDC) investigated the cases, drawing blood and cerebrospinal fluid (CSF) samples from the hospitals, and testing IgM antibody against JE using ELISA. We used Epi Data and Excel for data entry and analysis. RESULTS: A total of 1097 VEs were reported and 1053 (96.0%) had blood or CSF samples collected and tested for IgM antibody against JE. Three hundred and eleven cases (29.5%) showed JE antibody positive (JE confirmed case). Among the JE confirmed cases, numbers of those under 15 year of age accounted for 33.7%, 43.9% and 88.3% in Baoji, Weinan and Ankang prefectures respectively. The rest were mainly children aged 5-14 years old (53.3%). Toddlers,farmers and children accounted for 85.2% in JE confirmed cases. About half of other VE cases (51.0%) were students of all age. Data an investigation on 398 reported VE cases at discharge, showed that 67.1% of JE confirmed cases recovered while 83.7% of the other VE cases fully recovered. The case fatality rates were 9.2% for JE confirmed cases and 3.1% for other VE cases. 578 cases were followed up at 90-days after discharge, 69.6% of JE confirmed cases and 90.2% of other VE cases recovered, with case fatality rates were 13.6% and 3.6% for JE confirmed cases and for other VE cases, respectively. The sequelae rates were 10.0% for JE confirmed cases and 4.5% for other VE cases. CONCLUSION: The peak of the VE season was the same as that of JE. There were 45.6% of reported JE cases with negative JE IgM, suggesting that it is necessary to carry out laboratory testing for clinical diagnosis cases. The fact that high risk population was different at prefectures levels suggested that more attention be paid in JE control and prevention.