Construction of all-in-focus images assisted by depth sensing

Multi-focus image fusion is a technique for obtaining an all-in-focus image in which all objects are in focus to extend the limited depth of field (DoF) of an imaging system. Different from traditional RGB-based methods, this paper presents a new multi-focus image fusion method assisted by depth sensing. In this work, a depth sensor is used together with a color camera to capture images of a scene. A graph-based segmentation algorithm is used to segment the depth map from the depth sensor, and the segmented regions are used to guide a focus algorithm to locate in-focus image blocks from among multi-focus source images to construct the reference all-in-focus image. Five test scenes and six evaluation metrics were used to compare the proposed method and representative state-of-the-art algorithms. Experimental results quantitatively demonstrate that this method outperforms existing methods in both speed and quality (in terms of comprehensive fusion metrics). The generated images can potentially be used as reference all-in-focus images.Comment: 18 pages. This paper has been submitted to Computer Vision and Image Understandin

A Novel Method for Extrinsic Calibration of Multiple RGB-D Cameras Using Descriptor-Based Patterns

This letter presents a novel method to estimate the relative poses between RGB-D cameras with minimal overlapping fields of view in a panoramic RGB-D camera system. This calibration problem is relevant to applications such as indoor 3D mapping and robot navigation that can benefit from a 360$^\circ$ field of view using RGB-D cameras. The proposed approach relies on descriptor-based patterns to provide well-matched 2D keypoints in the case of a minimal overlapping field of view between cameras. Integrating the matched 2D keypoints with corresponding depth values, a set of 3D matched keypoints are constructed to calibrate multiple RGB-D cameras. Experiments validated the accuracy and efficiency of the proposed calibration approach, both superior to those of existing methods (800 ms vs. 5 seconds; rotation error of 0.56 degrees vs. 1.6 degrees; and translation error of 1.80 cm vs. 2.5 cm.Comment: 6 pages, 7 figures, under review by IEEE Robotics and Automation Letters & ICR

CMDFusion: Bidirectional Fusion Network with Cross-modality Knowledge Distillation for LIDAR Semantic Segmentation

2D RGB images and 3D LIDAR point clouds provide complementary knowledge for the perception system of autonomous vehicles. Several 2D and 3D fusion methods have been explored for the LIDAR semantic segmentation task, but they suffer from different problems. 2D-to-3D fusion methods require strictly paired data during inference, which may not be available in real-world scenarios, while 3D-to-2D fusion methods cannot explicitly make full use of the 2D information. Therefore, we propose a Bidirectional Fusion Network with Cross-Modality Knowledge Distillation (CMDFusion) in this work. Our method has two contributions. First, our bidirectional fusion scheme explicitly and implicitly enhances the 3D feature via 2D-to-3D fusion and 3D-to-2D fusion, respectively, which surpasses either one of the single fusion schemes. Second, we distillate the 2D knowledge from a 2D network (Camera branch) to a 3D network (2D knowledge branch) so that the 3D network can generate 2D information even for those points not in the FOV (field of view) of the camera. In this way, RGB images are not required during inference anymore since the 2D knowledge branch provides 2D information according to the 3D LIDAR input. We show that our CMDFusion achieves the best performance among all fusion-based methods on SemanticKITTI and nuScenes datasets. The code will be released at https://github.com/Jun-CEN/CMDFusion

A novel 7-chemokine-genes predictive signature for prognosis and therapeutic response in renal clear cell carcinoma

Background: Renal clear cell carcinoma (ccRCC) is one of the most prevailing type of malignancies, which is affected by chemokines. Chemokines can form a local network to regulate the movement of immune cells and are essential for tumor proliferation and metastasis as well as for the interaction between tumor cells and mesenchymal cells. Establishing a chemokine genes signature to assess prognosis and therapy responsiveness in ccRCC is the goal of this effort.Methods: mRNA sequencing data and clinicopathological data on 526 individuals with ccRCC were gathered from the The Cancer Genome Atlas database for this investigation (263 training group samples and 263 validation group samples). Utilizing the LASSO algorithm in conjunction with univariate Cox analysis, the gene signature was constructed. The Gene Expression Omnibus (GEO) database provided the single cell RNA sequencing (scRNA-seq) data, and the R package “Seurat” was applied to analyze the scRNA-seq data. In addition, the enrichment scores of 28 immune cells in the tumor microenvironment (TME) were calculated using the “ssGSEA” algorithm. In order to develop possible medications for patients with high-risk ccRCC, the “pRRophetic” package is employed.Results: High-risk patients had lower overall survival in this model for predicting prognosis, which was supported by the validation cohort. In both cohorts, it served as an independent prognostic factor. Annotation of the predicted signature’s biological function revealed that it was correlated with immune-related pathways, and the riskscore was positively correlated with immune cell infiltration and several immune checkpoints (ICs), including CD47, PDCD1, TIGIT, and LAG-3, while it was negatively correlated with TNFRSF14. The CXCL2, CXCL12, and CX3CL1 genes of this signature were shown to be significantly expressed in monocytes and cancer cells, according to scRNA-seq analysis. Furthermore, the high expression of CD47 in cancer cells suggested us that this could be a promising immune checkpoint. For patients who had high riskscore, we predicted 12 potential medications.Conclusion: Overall, our findings show that a putative 7-chemokine-gene signature might predict a patient’s prognosis for ccRCC and reflect the disease’s complicated immunological environment. Additionally, it offers suggestions on how to treat ccRCC using precision treatment and focused risk assessment

MICA: A fast short-read aligner that takes full advantage of Many Integrated Core Architecture (MIC)

Background: Short-read aligners have recently gained a lot of speed by exploiting the massive parallelism of GPU. An uprising alterative to GPU is Intel MIC; supercomputers like Tianhe-2, currently top of TOP500, is built with 48,000 MIC boards to offer ~55 PFLOPS. The CPU-like architecture of MIC allows CPU-based software to be parallelized easily; however, the performance is often inferior to GPU counterparts as an MIC card contains only ~60 cores (while a GPU card typically has over a thousand cores). Results: To better utilize MIC-enabled computers for NGS data analysis, we developed a new short-read aligner MICA that is optimized in view of MIC's limitation and the extra parallelism inside each MIC core. By utilizing the 512-bit vector units in the MIC and implementing a new seeding strategy, experiments on aligning 150 bp paired-end reads show that MICA using one MIC card is 4.9 times faster than BWA-MEM (using 6 cores of a top-end CPU), and slightly faster than SOAP3-dp (using a GPU). Furthermore, MICA's simplicity allows very efficient scale-up when multiple MIC cards are used in a node (3 cards give a 14.1-fold speedup over BWA-MEM). Summary: MICA can be readily used by MIC-enabled supercomputers for production purpose. We have tested MICA on Tianhe-2 with 90 WGS samples (17.47 Tera-bases), which can be aligned in an hour using 400 nodes. MICA has impressive performance even though MIC is only in its initial stage of development. Availability and implementation: MICA's source code is freely available at http://sourceforge.net/projects/mica-aligner under GPL v3. Supplementary information: Supplementary information is available as "Additional File 1". Datasets are available at www.bio8.cs.hku.hk/dataset/mica.published_or_final_versio

Immunoglobulin a vasculitis with testicular/epididymal involvement in children: A retrospective study of a ten-year period

The clinical characteristics and risk factors for testicular/epididymal involvement in 73 children with immunoglobulin A vasculitis (IgAV) who were admitted to our hospital between January 2012 and November 2022 were reviewed. The demographic data, laboratory parameters, and follow-up data of the patients were compared to those of 146 males without testicular/epididymal involvement. A logistic regression analysis was performed to determine the variables associated with testicular/epididymal involvement. The prevalence of testicular/epididymal involvement among male patients with IgAV was 1.3% (73/5,556). Increased blood flow in the testes and/or epididymis on ultrasound was found in 71 patients. The remaining two patients underwent surgical exploration for loss or reduction of testicular blood flow. One patient underwent orchiectomy for intraoperative confirmation of complete right testicular infarction. Pathological findings revealed IgA immune complex deposition in the testis. Patient age (odds ratio [OR] = 0.792; 95% confidence interval [CI]: 0.682–0.919, p = 0.002), platelet count (OR = 1.011; 95% CI: 1.002–1.020, p = 0.013), and immunoglobulin M (IgM) levels (OR = 0.236; 95% CI: 0.091–0.608, p = 0.003) were strongly associated with the occurrence of testicular/epididymal involvement in IgAV. Therefore, young age, increased platelet count, and low IgM levels in patients with IgAV are potential risk factors for testicular/epididymal involvement. Doppler ultrasound can help differentiate IgAV from acute scrotum. Most patients with testicular/epididymal involvement have good prognoses, although serious complications such as testicular infarction may occur

Whole exome sequencing identifies frequent somatic mutations in cell-cell adhesion genes in chinese patients with lung squamous cell carcinoma

Lung squamous cell carcinoma (SQCC) accounts for about 30% of all lung cancer cases. Understanding of mutational landscape for this subtype of lung cancer in Chinese patients is currently limited. We performed whole exome sequencing in samples from 100 patients with lung SQCCs to search for somatic mutations and the subsequent target capture sequencing in another 98 samples for validation. We identified 20 significantly mutated genes, including TP53, CDH10, NFE2L2 and PTEN. Pathways with frequently mutated genes included those of cell-cell adhesion/Wnt/Hippo in 76%, oxidative stress response in 21%, and phosphatidylinositol-3-OH kinase in 36% of the tested tumor samples. Mutations of Chromatin regulatory factor genes were identified at a lower frequency. In functional assays, we observed that knockdown of CDH10 promoted cell proliferation, soft-agar colony formation, cell migration and cell invasion, and overexpression of CDH10 inhibited cell proliferation. This mutational landscape of lung SQCC in Chinese patients improves our current understanding of lung carcinogenesis, early diagnosis and personalized therapy