Convolutional neural network classification of ultrasound images by liver fibrosis stages based on echo-envelope statistics

Introduction: Assessing the stage of liver fibrosis during the diagnosis and follow-up of patients with diffuse liver disease is crucial. The tissue structure in the fibrotic liver is reflected in the texture and contrast of an ultrasound image, with the pixel brightness indicating the intensity of the echo envelope. Therefore, the progression of liver fibrosis can be evaluated non-invasively by analyzing ultrasound images.Methods: A convolutional-neural-network (CNN) classification of ultrasound images was applied to estimate liver fibrosis. In this study, the colorization of the ultrasound images using echo-envelope statistics that correspond to the features of the images is proposed to improve the accuracy of CNN classification. In the proposed method, the ultrasound image is modulated by the 3rd- and 4th-order moments of pixel brightness. The two modulated images and the original image were then synthesized into a color image of RGB representation.Results and Discussion: The colorized ultrasound images were classified via transfer learning of VGG-16 to evaluate the effect of colorization. Of the 80 ultrasound images with liver fibrosis stages F1–F4, 38 images were accurately classified by the CNN using the original ultrasound images, whereas 47 images were classified by the proposed method

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

The role of genetic factors in HBV-related HCC: perspectives from local genetic backgrounds and clinical epidemiology

Familial clustering of hepatitis B surface antigen carriers (HBsAg) and hepatocellular carcinoma (HCC) has led to the evaluation of the role of genetics in hepatitis B-related diseases. Consistent reports indicate that the HLA-DP and -DQ loci are associated with persistent hepatitis B virus (HBV) infection. However, for hepatocarcinogenesis, existing studies have low power and conflicting data. Global single nucleotide polymorphism (SNP) data was collected from the 1000 Genomes Project and correlated with local epidemiological information. Southeastern Asia has a higher prevalence of HBsAg than Northeastern Asia; this was used in the evaluation of persistent HBV infection. The higher incidence of HCC in West Africa compared with East Africa was used in the evaluation of hepatocarcinogenesis. The allele frequencies for SNPs were significantly different between East Asians and Africans. Therefore, SNPs that have been identified in persistent HBV infections in East Asia may not be completely applicable in Africa. SNPs in NTCP, CTF19, and the HLA-DQ and -DP loci showed North-to-South allele frequency changes in East Asia. These findings confirm the role of genetics in persistent HBV infection. Some of the SNPs in the HLA loci show a trend of West-to-East allele frequency changes in Africa, indicating they may participate in hepatocarcinogenesis. Among the non-HLA related SNPs, rs2596542 in MICA shows a strong trend of allele frequency changes and is correlated with HCC incidence in Africa. SNPs in KIF1, IL-1A, and STAT4 also show, albeit with low statistical power, allele frequency trends compatible with HCC incidence. Taken together, there are strong correlations between background genetics in HLA-DP and -DQ loci with persistent HBV infection and hepatocarcinogenesis. The correlations were weak-positive in non-HLA loci

Hepatocellular carcinoma occurred in a Hepatitis B carrier clinic cohort during a mean follow up of 10 years

Aim: Chronic persistent hepatitis B virus carriers are generally asymptomatic until the advanced stage of the disease. The “Hepatitis B-Carrier Clinics” of Chang Gung Memorial Hospital has been using alpha-fetoprotein (AFP) and liver ultrasound for early detection of hepatocellular carcinoma (HCC) in hepatitis B surface antigen (HBsAg) carriers since 1980.Methods: We evaluated the results of surveillance between 1980 and 2012 by collecting clinic data, matched cancer registry status, and national mortality database status.Results: Of 15,235 HBsAg carriers, 238 instances of HCC (1.5% or 156.2/100,000 person-years) were detected over a mean follow-up period of 10.0 ± 7.6 years. There were more men (89.1%) and patients with liver cirrhosis (70.2%) in the HCC group (P < 0.001), and both the initial and maximal alanine aminotransferase (ALT) levels were higher in this group (P < 0.001). One hundred and thirty cases of HCC (54.6%) were identified during regular follow-up sessions, 55 (23.1%) were detected after the regular schedule had lapsed (“out-of-schedule”), and 53 (22.3%) were lost to follow-up completely. The mean tumor size was smaller in the regular group than in the out-of-schedule group (2.72 cm vs. 4.59 cm, P < 0.001), and the survival rate was higher (43.8% vs. 30.9%, P < 0.001).Conclusion: The incidence of HCC was relatively low in the HBsAg-Carrier Clinics cohort. Surveillance for early diagnosis of HCC improved the survival of high-risk HBsAg carriers. To ensure cost-effectiveness, we suggest using different screening strategies according to the individual risk of hepatocarcinogenesis