Automatic Kidney and Tumor Segmentation with Attention-based V-Net

Deep learning, especially Convolutional Neural Networks (CNNs) have been implemented to resolve a variety of both computer vision and medical image analysis problems recently. Among a rather wide range of Segmentation CNNs, V-Net is a relatively popular one, which is also an extended version of U-Net which processes 2D images. In this work, we propose an innovative V-Net with a embeded attention module. Inspired by spatial neural attention for generating pseudo-annotations, we modify the Decoupled attention into 3D version and insert it into the V-Net. This CNN network is trained end-to-end on CT volumes, and able to learn to predict segmentation blocks for a certain case. The definition of “block” will be elaborated in Section 3. Finally, the blocks will be concatenated to create a complete segmentation for a single case

Genome sequence of the tsetse fly (Glossina morsitans):Vector of African trypanosomiasis

Tsetse flies are the sole vectors of human African trypanosomiasis throughout sub-Saharan Africa. Both sexes of adult tsetse feed exclusively on blood and contribute to disease transmission. Notable differences between tsetse and other disease vectors include obligate microbial symbioses, viviparous reproduction, and lactation. Here, we describe the sequence and annotation of the 366-megabase Glossina morsitans morsitans genome. Analysis of the genome and the 12,308 predicted protein-encoding genes led to multiple discoveries, including chromosomal integrations of bacterial (Wolbachia) genome sequences, a family of lactation-specific proteins, reduced complement of host pathogen recognition proteins, and reduced olfaction/chemosensory associated genes. These genome data provide a foundation for research into trypanosomiasis prevention and yield important insights with broad implications for multiple aspects of tsetse biology.IS

Functional analysis of the promoter of an early zygotic gene KLC2 in Aedes aegypti

Abstract Background Aedes aegypti is an important mosquito vector that transmits arboviruses that cause devastating diseases including Zika, dengue fever, yellow fever and chikungunya. Improved understanding of gene regulation in the early development of Ae. aegypti will facilitate genetic studies and help the development of novel control strategies of this important disease vector. Results In this study, we demonstrated through transgenic assays that the promoter of an endogenous early zygotic gene KLC2 could drive gene expression in the syncytial blastoderm and early cellular blastoderm, which is a stage that the developing germline and the rest of embryo are accessible to genetic manipulation. An unexpected expression of the reporter gene in transgenic male testes was also observed. Further analysis confirmed the expression of the endogenous KLC2 in the testes, which was not detected in the previous RNA sequencing data. Conclusions Our finding provided a new promoter element that can be used in future genetic studies and applications in Ae. aegypti. Moreover, our transgenic reporter assays showed that cautions are needed when interpreting RNA sequencing data as transient or tissue-specific transcription may go undetected by RNAseq

Identification of early zygotic genes in the yellow fever mosquito Aedes aegypti and discovery of a motif involved in early zygotic genome activation.

During early embryogenesis the zygotic genome is transcriptionally silent and all mRNAs present are of maternal origin. The maternal-zygotic transition marks the time over which embryogenesis changes its dependence from maternal RNAs to zygotically transcribed RNAs. Here we present the first systematic investigation of early zygotic genes (EZGs) in a mosquito species and focus on genes involved in the onset of transcription during 2-4 hr. We used transcriptome sequencing to identify the "pure" (without maternal expression) EZGs by analyzing transcripts from four embryonic time ranges of 0-2, 2-4, 4-8, and 8-12 hr, which includes the time of cellular blastoderm formation and up to the start of gastrulation. Blast of 16,789 annotated transcripts vs. the transcriptome reads revealed evidence for 63 (P<0.001) and 143 (P<0.05) nonmaternally derived transcripts having a significant increase in expression at 2-4 hr. One third of the 63 EZG transcripts do not have predicted introns compared to 10% of all Ae. aegypti genes. We have confirmed by RT-PCR that zygotic transcription starts as early as 2-3 hours. A degenerate motif VBRGGTA was found to be overrepresented in the upstream sequences of the identified EZGs using a motif identification software called SCOPE. We find evidence for homology between this motif and the TAGteam motif found in Drosophila that has been implicated in EZG activation. A 38 bp sequence in the proximal upstream sequence of a kinesin light chain EZG (KLC2.1) contains two copies of the mosquito motif. This sequence was shown to support EZG transcription by luciferase reporter assays performed on injected early embryos, and confers early zygotic activity to a heterologous promoter from a divergent mosquito species. The results of these studies are consistent with the model of early zygotic genome activation via transcriptional activators, similar to what has been found recently in Drosophila

amaximumpowerpointtrackerforphotovoltaicenergysystemsbasedonfuzzyneuralnetworks

To extract the maximum power from a photovoltaic （PV） energy system, the real-time maximum power point （MPP） of the PV array must be tracked closely. The non-linear and time-variant characteristics of the PV array and the non-linear and non-minimum phase characteristics of a boost converter make it difficult to track the MPP for traditional control strategies. We propose a fuzzy neural network controller （FNNC）, which combines the reasoning capability of fuzzy logical systems and the learning capability of neural networks, to track the MPP. With a derived learning algorithm, the parameters of the FNNC are updated adaptively. A gradient estimator based on a radial basis function neural network is developed to provide the reference information to the FNNC. Simulation results show that the proposed control algorithm provides much better tracking performance compared with the filzzy logic control algorithm

VisComposer: A Visual Programmable Composition Environment for Information Visualization

As the amount of data being collected has increased, the need for tools that can enable the visual exploration of data has also grown. This has led to the development of a variety of widely used programming frameworks for information visualization. Unfortunately, such frameworks demand comprehensive visualization and coding skills and require users to develop visualization from scratch. An alternative is to create interactive visualization design environments that require little to no programming. However, these tools only supports a small portion of visual forms.We present a programmable integrated development environment (IDE), VisComposer, that supports the development of expressive visualization using a drag-and-drop visual interface. VisComposer exposes the programmability by customizing desired components within a modularized visualization composition pipeline, effectively balancing the capability gap between expert coders and visualization artists. The implemented system empowers users to compose comprehensive visualizations with real-time preview and optimization features, and supports prototyping, sharing and reuse of the effects by means of an intuitive visual composer. Visual programming and textual programming integrated in our system allow users to compose more complex visual effects while retaining the simplicity of use. We demonstrate the performance of VisComposer with a variety of examples and an informal user evaluation. Keywords: Information Visualization, Visualization authoring, Interactive development environmen

Pure early zygotic genes in the Asian malaria mosquito Anopheles stephensi

Abstract Background The Asian malaria mosquito, Anopheles stephensi, is a major urban malaria vector in the Middle East and on the Indian subcontinent. Early zygotic transcription, which marks the maternal-to-zygotic transition, has not been systematically studied in An. stephensi or any other Anopheles mosquitoes. Improved understanding of early embryonic gene expression in An. stephensi will facilitate genetic and evolutionary studies and help with the development of novel control strategies for this important disease vector. Results We obtained RNA-seq data in biological triplicates from four early An. stephensi embryonic time points. Using these data, we identified 70 and 153 pure early zygotic genes (pEZGs) under stringent and relaxed conditions, respectively. We show that these pEZGs are enriched in functional groups related to DNA-binding transcription regulators, cell cycle modulators, proteases, transport, and cellular metabolism. On average these pEZGs are shorter and have less introns than other An. stephensi genes. Some of the pEZGs may arise de novo while others have clear non-pEZG paralogs. There is no or very limited overlap between An. stephensi pEZGs and Drosophila melanogaster or Aedes aegypti pEZGs. Interestingly, the upstream region of An. stephensi pEZGs lack significant enrichment of a previously reported TAGteam/VBRGGTA motif found in the regulatory region of pEZGs in D. melanogaster and Ae. aegypti. However, a GT-rich motif was found in An. stephensi pEZGs instead. Conclusions We have identified a number of pEZGs whose predicted functions and structures are consistent with their collective roles in the degradation of maternally deposited components, activation of the zygotic genome, cell division, and metabolism. The pEZGs appear to rapidly turn over within the Dipteran order and even within the Culicidae family. These pEZGs, and the shared regulatory motif, could provide the promoter or regulatory sequences to drive gene expression in the syncytial or early cellular blastoderm, a period when the developing embryo is accessible to genetic manipulation. In addition, these molecular resources may be used to achieve sex separation of mosquitoes for sterile insect technique