A multi-view latent variable model reveals cellular heterogeneity in complex tissues for paired multimodal single-cell data

Motivation Single-cell multimodal assays allow us to simultaneously measure two different molecular features of the same cell, enabling new insights into cellular heterogeneity, cell development and diseases. However, most existing methods suffer from inaccurate dimensionality reduction for the joint-modality data, hindering their discovery of novel or rare cell subpopulations. Results Here, we present VIMCCA, a computational framework based on variational-assisted multi-view canonical correlation analysis to integrate paired multimodal single-cell data. Our statistical model uses a common latent variable to interpret the common source of variances in two different data modalities. Our approach jointly learns an inference model and two modality-specific non-linear models by leveraging variational inference and deep learning. We perform VIMCCA and compare it with 10 existing state-of-the-art algorithms on four paired multi-modal datasets sequenced by different protocols. Results demonstrate that VIMCCA facilitates integrating various types of joint-modality data, thus leading to more reliable and accurate downstream analysis. VIMCCA improves our ability to identify novel or rare cell subtypes compared to existing widely used methods. Besides, it can also facilitate inferring cell lineage based on joint-modality profiles

Tridimensional Reconstruction Applied to Cultural Heritage with the Use of Camera-Equipped UAV and Terrestrial Laser Scanner

No single sensor can acquire complete information by applying one or several multi-surveys to cultural object reconstruction. For instance, a terrestrial laser scanner (TLS) usually obtains information on building facades, whereas aerial photogrammetry is capable of providing the perspective for building roofs. In this study, a camera-equipped unmanned aerial vehicle system (UAV) and a TLS were used in an integrated design to capture 3D point clouds and thus facilitate the acquisition of whole information on an object of interest for cultural heritage. A camera network is proposed to modify the image-based 3D reconstruction or structure from motion (SfM) method by taking full advantage of the flight control data acquired by the UAV platform. The camera network improves SfM performances in terms of image matching efficiency and the reduction of mismatches. Thus, this camera network modified SfM is employed to process the overlapping UAV image sets and to recover the scene geometry. The SfM output covers most information on building roofs, but has sparse resolution. The dense multi-view 3D reconstruction algorithm is then applied to improve in-depth detail. The two groups of point clouds from image reconstruction and TLS scanning are registered from coarse to fine with the use of an iterative method. This methodology has been tested on one historical monument in Fujian Province, China. Results show a final point cloud with complete coverage and in-depth details. Moreover, findings demonstrate that these two platforms, which integrate the scanning principle and image reconstruction methods, can supplement each other in terms of coverage, sensing resolution, and model accuracy to create high-quality 3D recordings and presentations

Results of meta-analysis of increased CCAT1 expression and clinicopathological features in various cancers.

<p>Results of meta-analysis of increased CCAT1 expression and clinicopathological features in various cancers.</p

Meta-analysis of the independent role of CCAT1 in OS and recurrence of different types of cancer after excluding the outlier study.

<p>Meta-analysis of the independent role of CCAT1 in OS and recurrence of different types of cancer after excluding the outlier study.</p

Meta-analysis of the pooled HRs of OS of different types of cancer with increased CCAT1 expression.

<p>(A) Subgroup analysis of HRs of OS by factor of sample size. (B) Subgroup analysis of HRs of OS by factor of type of cancer. (C) Subgroup analysis of HRs of OS by factor of preoperative treatment. (D) Subgroup analysis of HRs of OS by factor of paper quality.</p

Prognostic value of long non-coding RNA CCAT1 expression in patients with cancer: A meta-analysis

<div><p>Background</p><p>LncRNA CCAT1 is significantly overexpressed in various types of cancers, suggesting that it might be associated with prognosis and clinicopathological features in patients with cancer.</p><p>Methods</p><p>A comprehensive search was performed in Pubmed, Web of Science, OVID and CNKI databases. We also retrieved articles from other sources, such as retrieving from the reference lists of relevant articles. Eligible studies were included based on defined exclusion and inclusion criteria to perform a meta-analysis. STATA 14.0 was used to estimate pooled hazard ratios (HRs) with 95% confidence interval (95% CI), the heterogeneity among studies and publication bias to judge the prognostic value.</p><p>Results</p><p>A total of 1587 patients from 11 eligible studies were included in the meta-analysis. The results showed that high expression level of CCAT1 was significantly associated with shorter overall survival in cancer patients (HR 2.335, 95% CI:1.551–3.517); in the subgroup analysis, region (China or UK), sample size (more or less than 100), type of cancer (digestive or non-digestive disease) and paper quality (score more or less than 7) did not alter the association between CCAT1 expression and cancer prognosis but preoperative treatment did. And CCAT1 expression was an independent prognostic marker for overall survival in patients with cancer (pooled HR 2.195, 95%CI:1.316–3.664) using Cox multivariate analyses. The clinicopathological parameters analysis further showed that increased expression level of CCAT1 was correlated with tumor size, lymph node metastasis, TNM stage, distant metastasis, microvascular invasion and capsular formation in relevant cancers.</p><p>Conclusions</p><p>The meta-analysis results from present study suggested that increased expression level of CCAT1 was associated with poor prognosis and can serve as an independent biomarker. And the expression level of CCAT1 was associated with clinicopathological features in relevant cancers.</p></div

Results of subgroup analysis of pooled hazard ratios of overall survival of different types of cancer with increased CCAT1 expression.

<p>Results of subgroup analysis of pooled hazard ratios of overall survival of different types of cancer with increased CCAT1 expression.</p

Characteristics of studies included in the meta-analysis.

<p>Characteristics of studies included in the meta-analysis.</p

Association of COL9A3 trp3 polymorphism with intervertebral disk degeneration: a meta-analysis

Abstract Background Intervertebral disk degeneration (IDD) is a common musculoskeletal disease associated with genetic factors. COL9A3 gene encodes the α3 (IX) chain of type IX collagen that is part of the interior structure of the disc. Mutations in COL9A3 gene sequence, leading to an Arg103Trp substitution in its 3 chain (the Trp3 allele at rs61734651 site), respectively, have been found to be connected with IDD occurrence in several studies. However, those studies have showed conflict results. Thus, a meta-analysis has been performed to assess the associations between the COL9A3 trp3 polymorphism and IDD. Methods Data were gathered from the following four electronic databases: PubMed, Web of Science (WOS), Embase and Cochrane library up to January 01, 2018. The pooled odds ratio (polled ORs) and 95% confidence interval (CI) were calculated to evaluate the strength of relationship between the COL9A3 trp3 polymorphism and IDD. Results Eleven eligible studies with 1631 cases of IDD and 1366 controls were included in this meta-analysis. The results indicated that the COL9A3 trp3 polymorphism was not associated with IDD (trp3 positive versus trp3 negative: OR = 1.31, 95%CI = 0.78–2.21, P = 0.309). Furthermore, the Egger’s test and the Begg funnel plot did not show any evidence of publication bias. Conclusions Our results suggest that the COL9A3 trp3 polymorphism might not be associated with IDD. Nor did we find any relationship in subgroup analyses stratified by gender and ethnicity. Future researches with larger samples are required to verify this outcome

Mesenchymal Stem Cells Protect Nucleus Pulposus Cells from Compression-Induced Apoptosis by Inhibiting the Mitochondrial Pathway

Objective. Excessive apoptosis of nucleus pulposus cells (NPCs) induced by various stresses, including compression, contributes to the development of intervertebral disc degeneration (IVDD). Mesenchymal stem cells (MSCs) can benefit the regeneration of NPCs and delay IVDD, but the underlying molecular mechanism is poorly understood. This study aimed to evaluate the antiapoptosis effects of bone marrow-derived MSC (BMSC) on rat NPCs exposed to compression and investigate whether the mitochondrial pathway was involved. Methods. BMSCs and NPCs were cocultured in the compression apparatus at 1.0 MPa for 36 h. Cell viability, apoptosis, mitochondrial function, and the expression of apoptosis-related proteins were evaluated. Results. The results showed that coculturing with BMSCs increased the cell viability and reduced apoptosis of NPCs exposed to compression. Meanwhile, BMSCs could relieve the compression-induced mitochondrial damage of NPCs by decreasing reactive oxygen species level and maintaining mitochondrial membrane potential as well as mitochondrial integrity. Furthermore, coculturing with BMSCs suppressed the activated caspase-3 and activated caspase-9, decreased the expressions of cytosolic cytochrome c and Bax, and increased the expression of Bcl-2. Conclusions. Our results suggest that BMSCs can protect against compression-induced apoptosis of NPCs by inhibiting the mitochondrial pathway and thus enhance our understanding on the MSC-based therapy for IVDD