Unsupervised learning for cross-domain medical image synthesis using deformation invariant cycle consistency networks

Recently, the cycle-consistent generative adversarial networks (CycleGAN) has been widely used for synthesis of multi-domain medical images. The domain-specific nonlinear deformations captured by CycleGAN make the synthesized images difficult to be used for some applications, for example, generating pseudo-CT for PET-MR attenuation correction. This paper presents a deformation-invariant CycleGAN (DicycleGAN) method using deformable convolutional layers and new cycle-consistency losses. Its robustness dealing with data that suffer from domain-specific nonlinear deformations has been evaluated through comparison experiments performed on a multi-sequence brain MR dataset and a multi-modality abdominal dataset. Our method has displayed its ability to generate synthesized data that is aligned with the source while maintaining a proper quality of signal compared to CycleGAN-generated data. The proposed model also obtained comparable performance with CycleGAN when data from the source and target domains are alignable through simple affine transformations

Evidence from Ab Initio and Transport Modeling for Diffusion-Driven Zirconium Isotopic Fractionation in Igneous Rocks

We use density functional theory to calculate the equilibrium isotopic fractionation factors of zirconium (Zr) in a variety of minerals including zircon, baddeleyite, Ca-catapleiite, ilmenite, geikielite, magnetite, apatite, K-feldspar, quartz, olivine, clinopyroxene, orthopyroxene, amphibole, and garnet. We also report equilibrium isotopic fractionation factors for Hf in zircons, Ca-catapleiite, and ilmenite. These calculations show that coordination environment is an important control on Zr and Hf isotopic fractionation, with minerals with Zr and Hf in low coordinations predicted to be enriched in the heavy isotopes of Zr and Hf, relative to those with Zr and Hf in high coordinations. At equilibrium, zircon, which hosts Zr and Hf in 8-fold coordination, is predicted to have low 94Zr/90Zr and 179Hf/177Hf ratios compared to silicate melt, which hosts Zr and Hf in 6-fold coordination. However, our modeling results indicate that little equilibrium isotopic fractionation for Zr is expected during magmatic differentiation and zircon crystallization. We show through isotopic transport modeling that the Zr isotopic variations that were documented in igneous rocks are likely due to diffusion-driven kinetic isotopic fractionation. The two settings where this could take place are (i) diffusion-limited crystallization of zircon (DLC model) and (ii) diffusion-triggered crystallization of zircon (DTC model) in the boundary layer created by the growth of Zr-poor minerals. Fractional crystallization of zircons enriched in light Zr isotopes by diffusion can drive residual magmas toward heavy Zr isotopic compositions. Our diffusive transport model gives the framework to interpret Zr isotope data and gain new insights into the cooling history of igneous rocks and the setting of zircon crystallization

Prevalence and trend of hepatitis C virus infection among blood donors in Chinese mainland: a systematic review and meta-analysis

<p>Abstract</p> <p>Background</p> <p>Blood transfusion is one of the most common transmission pathways of hepatitis C virus (HCV). This paper aims to provide a comprehensive and reliable tabulation of available data on the epidemiological characteristics and risk factors for HCV infection among blood donors in Chinese mainland, so as to help make prevention strategies and guide further research.</p> <p>Methods</p> <p>A systematic review was constructed based on the computerized literature database. Infection rates and 95% confidence intervals (95% CI) were calculated using the approximate normal distribution model. Odds ratios and 95% CI were calculated by fixed or random effects models. Data manipulation and statistical analyses were performed using STATA 10.0 and ArcGIS 9.3 was used for map construction.</p> <p>Results</p> <p>Two hundred and sixty-five studies met our inclusion criteria. The pooled prevalence of HCV infection among blood donors in Chinese mainland was 8.68% (95% CI: 8.01%-9.39%), and the epidemic was severer in North and Central China, especially in Henan and Hebei. While a significant lower rate was found in Yunnan. Notably, before 1998 the pooled prevalence of HCV infection was 12.87% (95%CI: 11.25%-14.56%) among blood donors, but decreased to 1.71% (95%CI: 1.43%-1.99%) after 1998. No significant difference was found in HCV infection rates between male and female blood donors, or among different blood type donors. The prevalence of HCV infection was found to increase with age. During 1994-1995, the prevalence rate reached the highest with a percentage of 15.78% (95%CI: 12.21%-19.75%), and showed a decreasing trend in the following years. A significant difference was found among groups with different blood donation types, Plasma donors had a relatively higher prevalence than whole blood donors of HCV infection (33.95% <it>vs </it>7.9%).</p> <p>Conclusions</p> <p>The prevalence of HCV infection has rapidly decreased since 1998 and kept a low level in recent years, but some provinces showed relatively higher prevalence than the general population. It is urgent to make efficient measures to prevent HCV secondary transmission and control chronic progress, and the key to reduce the HCV incidence among blood donors is to encourage true voluntary blood donors, strictly implement blood donation law, and avoid cross-infection.</p

Pan-cancer analysis of whole genomes

Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale(1-3). Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter(4); identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation(5,6); analyses timings and patterns of tumour evolution(7); describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity(8,9); and evaluates a range of more-specialized features of cancer genomes(8,10-18).Peer reviewe

Evidence from Ab Initio and Transport Modeling for Diffusion-Driven Zirconium Isotopic Fractionation in Igneous Rocks

We use density functional theory to calculate the equilibrium isotopic fractionation factors of zirconium (Zr) in a variety of minerals including zircon, baddeleyite, Ca-catapleiite, ilmenite, geikielite, magnetite, apatite, K-feldspar, quartz, olivine, clinopyroxene, orthopyroxene, amphibole, and garnet. We also report equilibrium isotopic fractionation factors for Hf in zircons, Ca-catapleiite, and ilmenite. These calculations show that coordination environment is an important control on Zr and Hf isotopic fractionation, with minerals with Zr and Hf in low coordinations predicted to be enriched in the heavy isotopes of Zr and Hf, relative to those with Zr and Hf in high coordinations. At equilibrium, zircon, which hosts Zr and Hf in 8-fold coordination, is predicted to have low 94Zr/90Zr and 179Hf/177Hf ratios compared to silicate melt, which hosts Zr and Hf in 6-fold coordination. However, our modeling results indicate that little equilibrium isotopic fractionation for Zr is expected during magmatic differentiation and zircon crystallization. We show through isotopic transport modeling that the Zr isotopic variations that were documented in igneous rocks are likely due to diffusion-driven kinetic isotopic fractionation. The two settings where this could take place are (i) diffusion-limited crystallization of zircon (DLC model) and (ii) diffusion-triggered crystallization of zircon (DTC model) in the boundary layer created by the growth of Zr-poor minerals. Fractional crystallization of zircons enriched in light Zr isotopes by diffusion can drive residual magmas toward heavy Zr isotopic compositions. Our diffusive transport model gives the framework to interpret Zr isotope data and gain new insights into the cooling history of igneous rocks and the setting of zircon crystallization

PEDOT:PSS for flexible and stretchable electronics : modifications, strategies, and applications

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