scFSNN: a feature selection method based on neural network for single-cell RNA-seq data.

While single-cell RNA sequencing (scRNA-seq) allows researchers to analyze gene expression in individual cells, its unique characteristics like over-dispersion, zero-inflation, high gene-gene correlation, and large data volume with many features pose challenges for most existing feature selection methods. In this paper, we present a feature selection method based on neural network (scFSNN) to solve classification problem for the scRNA-seq data. scFSNN is an embedded method that can automatically select features (genes) during model training, control the false discovery rate of selected features and adaptively determine the number of features to be eliminated. Extensive simulation and real data studies demonstrate its excellent feature selection ability and predictive performance.

Protective Role of Endothelial SIRT1 in Deep Vein Thrombosis and Hypoxia-induced Endothelial Dysfunction Mediated by NF-κB Deacetylation.

Venous hypoxia is considered as the major pathogenetic mechanism linking blood flow stagnancy with deep vein thrombosis (DVT). Our previous study showed that activating SIRT1 may attenuate inferior vena cava (IVC) stenosis-induced DVT in rats. This study was aimed to investigate the role of endothelial SIRT1 in DVT and hypoxia-induced endothelial dysfunction as well as the underlying mechanism. Protein profiling of IVCs and blood plasma of DVT rats induced by IVC stenosis was analysed by 4D Label free proteomics analysis. To verify the independent role of SIRT1 in DVT and oxygen-glucose deprivation (OGD)-induced endothelial dysfunction, SIRT1 specific activator SRT1720 and SIRT1 knockdown in both local IVCs and endothelial cells were employed. Moreover, the role of the NF-κB were investigated using NF-κB inhibitor caffeic acid phenethyl ester (CAPE). SRT1720 significantly inhibited thrombus burden, leukocytes infiltration, protein expressions of cell adhesion molecules and chemokines, as well as acetylation level of NF-κB/p65 in wild DVT rats, while these protective effects of SRT1720 were abolished in rats with SIRT1 knockdown in local IVCs. In vitro, SRT1720 protected endothelial cells against OGD-induced dysfunction characterized with enhanced adhesion of monocytes as well as the protein expressions of cell adhesion molecules and chemokines, whereas these protective effects of SRT1720 were vanished by SIRT1 stable knockdown. Furthermore, CAPE attenuated endothelial cell dysfunction and abolished these effects of SIRT1 knockdown. Collectively, these data suggested that endothelial SIRT1 plays an independent role in ameliorating hypoxia-induced endothelial dysfunction and thrombotic inflammation in DVT, and this effect is mediated by NF-κB deacetylation.

Dissolved organic carbon response to hydrological drought characteristics: Based on long-term measurements of headwater streams.

Influence of extreme hydrological events on water quality has been widely concerned. For instance, droughts can inhibit dissolved organic carbon (DOC) exports or imports. However, the response relationship of DOC to hydrological drought characteristics (i.e., duration and severity) requires more in-depth research. We propose an integrated framework for constructing, validating, and applying the response relationship model, and investigate the capability of response model to simulate DOC based on hydrological drought characteristics. Three headwater basins (HP3a, HP4, and HP6), with different drainage areas (9.28-122.80 ha) and long-term (>40 year) observed DOC concentration and hydrometeorological data, in Harp Lake catchment, south-central Ontario, southeastern Canada, are used to demonstrate the proposed framework. Run theory and variable drought thresholds (VDTs) are used to identify hydrological drought characteristics, and DOC during hydrological drought is extracted. Based on the extracted hydrological drought characteristics and DOC for one basin (i.e., HP3a), the response relationship model is constructed and validated, and then applied to other two basins (i.e., HP4 and HP6). Three evaluation indicators: coefficient of determination (R2), root-mean-square-error (RMSE), and mean absolute percentage error (MAPE), are served to test the goodness-of-fit performance of the response relationship model. The results show that (i) annual DOC concentration showed a significant (a = 0.01) increasing trend during 1978-2018 in the study basin. (ii) During the hydrological drought, the variation of temperature affected DOC variation indirectly through direct influence on SO4 variation. (iii) The response sensitivity of DOC to hydrologic process with different timescales is varying within a year, namely, there is a larger response sensitivity from March to May than in other months. (iv) DOC during the hydrological drought has a close and regular linear relationship with hydrological drought characteristics, i.e., with the increase of drought duration and severity, DOC concentration also increases. The relationship with drought duration is better than that of severity (R2 = 0.92 vs 0.35). (v) The response relationship model (autoregressive integrated moving average) can simulate DOC in hydrological drought (R2 ≥ 0.87, RMSE ≤ 0.86, MAPE ≤ 13.69%) at HP3a, and also has good applications at HP4 and HP6 basins. These results provide an improved understanding of DOC-drought relationship, and may support policy makers that look for increased resilience of aquatic ecological security to droughts.

Temporary Upregulation of Nrf2 by Naringenin Alleviates Oxidative Damage in the Retina and ARPE-19 Cells.

Dry age-related macular degeneration (dAMD) is a chronic degenerative ophthalmopathy that leads to serious burden of visual impairment. Antioxidation in retinal pigment epithelium (RPE) cells is considered as a potential treatment for dAMD. Our previous studies have showed that naringenin (NAR) protects RPE cells from oxidative damage partly through SIRT1-mediated antioxidation. In this study, we tested the hypothesis that the Nrf2 signaling is another protective mechanism of NAR on dAMD. NaIO3-induced mouse retinopathy and ARPE-19 cell injury models were established. Immunochemical staining, immunofluorescence, and western blotting were performed to detect the protein expressions of Nrf2 and HO-1. In addition, ML385 (activity inhibitor of Nrf2) and zinc protoporphyrin (ZnPP, activity inhibitor of HO-1) were applied to explore the effect of NaIO3 or NAR. The results showed that NAR increased the protein expressions of Nrf2 and HO-1 in the retinas in mice exposed to NaIO3 at the early stage. NAR treatment also resulted in a stronger activation of Nrf2 at the early stage in NaIO3-treated ARPE-19 cells. Moreover, inhibition of HO-1 by ZnPP weakened the cytoprotective effect of NAR. The constitutive accumulation and activation of Nrf2 induced by NaIO3 led to the death of RPE cells. However, NAR decreased the protein expressions of Nrf2 and HO-1 towards normal level in the mouse retinas and ARPE-19 cells exposed to NaIO3 at the late stage. Our findings indicate that NAR protects RPE cells from oxidative damage via activating the Nrf2 signaling pathway.

Aqueous extract of Paeoniae Radix Rubra prevents deep vein thrombosis by ameliorating inflammation through inhibiting GSK3ß activity.

BACKGROUND: Deep vein thrombosis (DVT) is a kind of blood stasis syndrome. Paeoniae Radix Rubra (PRR) has long been widely used for eliminating blood stasis in China, but its effect on DVT has not yet been reported. PURPOSE: The present study aimed to assess the potential inhibitory effect of the aqueous extract of PRR (i.e.,PRR dispensing granule, PRRDG) on DVT and explore the underlying mechanism. STUDY DESIGN/METHODS: The chemical profile of PRRDG was analyzed by high-performance liquid chromatography. Sprague-Dawley rats were intragastrically treated with PRRDG (0.625, 1.25 and 1.875 g crude drug/kg/d) once daily for 7 consecutive days. On the sixth day, a model of inferior vena cava (IVC) stenosis-induced DVT was established. All rats were sacrificed on the seventh day. Serum was collected for enzyme-linked immunosorbent assay. Thrombus-containing IVC was weighed and further processed for histopathologic examination, immunohistochemical analysis and western blotting. LiCl and LY294002 were adopted to block and increase the activity of glycogen synthase kinase 3ß (GSK3ß), respectively. RESULTS: The chemical profile analysis showed that paeoniflorin, benzoylpaeoniflorin, albiflorin, gallic acid and catechin were the main constituents of PRRDG. LiCl decreased thrombus weight, reduced the number of inflammatory cells in thrombus and vein wall, down-regulated phosphorylated NF-κB p65 (p-p65) protein expression. Similarly, PRRDG decreased thrombus weight and tissue factor (TF) protein expression. PRRDG reduced the protein expression levels of P-selectin, monocyte chemoattractant protein-1 (MCP-1), intercellular cell adhesion molecule-1 (ICAM-1) and vascular cell adhesion molecule-1 (VCAM-1) in venous endothelium, serum levels of tumor necrosis factor-α (TNF-α) and interleukin-1ß (IL-1ß), and the number of inflammatory cells in thrombus and vein wall. Moreover, PRRDG down-regulated p-p65 protein expression and up-regulated phosphorylated GSK3ß (p-GSK3ß) protein expression. LY294002 abrogated the inhibitory effects of PRRDG on thrombus weight, TF protein expression, TNF-α and IL-1ß serum levels, inflammatory cells influxes, and p-p65 protein expression. CONCLUSION: PRRDG prevents DVT by ameliorating inflammation through inhibiting GSK3ß activity.

Naringenin protects RPE cells from NaIO3-induced oxidative damage in vivo and in vitro through up-regulation of SIRT1.

BACKGROUND: Dry age-related macular degeneration (dAMD) leads to serious burden of visual impairment and there is no definitive treatment. Previous studies have showed that naringenin (NAR) significantly increased electroretinography (ERG) c-wave in sodium iodate (NaIO3)-treated rats and viability of NaIO3-treated ARPE-19 cells. But the underlying mechanism is still unknown. PURPOSE: We tested the hypothesis that anti-oxidation mediated by Sirtuin 1 (SIRT1) was important to the protective effect of NAR on dAMD. STUDY DESIGN/METHODS: NaIO3-induced mice retinopathy and ARPE-19 cells injury models were established. In vivo, the protective effect of NAR eye drops on retina was evaluated by flash ERG (FERG) recording and histopathological examination. In vitro, viability of ARPE-19 cells, and the levels of lactic dehydrogenase (LDH), reactive oxygen species (ROS) and carbonyl protein were detected. Protein expression of SIRT1 was analyzed by immunochemical staining, immunofluorescence and western blotting. RESULTS: NAR eye drops improved retinal function and morphology and normalized the protein expression of SIRT1 in mice exposed to NaIO3. NAR promoted the survival of ARPE-19 cells in a concentration-dependent manner. NAR up-regulated SIRT1 protein expression, and decreased levels of ROS and carbonyl protein. Moreover, EX527, a selective inhibitor of SIRT1, abolished the effects of NAR on the cell viability and ROS. In addition, SRT1720, a selective agonist of SIRT1, improved the viability of cells and suppressed the production of ROS. CONCLUSION: Our findings indicate that SIRT1-mediated anti-oxidation contributes to the protective effect of NAR eye drops on dAMD.

Aqueous extract of Whitmania pigra Whitman ameliorates ferric chloride-induced venous thrombosis in rats via antioxidation.

Whitmania pigra Whitman (W. pigra) has been widely employed in decoction for the treatment of blood stasis syndrome for many years in China. The aim of the present study was to explore the anti-venous thrombosis (VT) mechanism of the aqueous extract of W. pigra (AEW) in rats. Rats were orally administered with AEW. A inferior vena cava (IVC) thrombosis model was established. Thrombosed IVC was weighed and histopathological analyses were performed. Blood coagulation, blood fibrinolysis, blood cell count, blood viscosity and platelet activity were evaluated. Reactive oxygen species (ROS) accumulation was analyzed. Malondialdehyde (MDA) content in thrombosed IVC and antioxidants in serum were detected. Protein expression of nuclear factor erythroid 2-related factor 2 (Nrf2) and heme oxygenase 1 (HO-1) in thrombosed IVC was determined. AEW significantly reduced thrombus weight. It did not affect blood coagulation, blood fibrinolysis, blood cell count, platelet activity, or whole blood viscosity. However, AEW remarkably alleviated vascular injury, reduced ROS accumulation and MDA content, enhanced the total antioxidant capacity and the activities of superoxide dismutase, glutathione peroxidase and glutathione reductase. It increased the glutathione/oxidized glutathione ratio and the protein expression levels of Nrf2 and HO-1. In summary, W. pigra may prevent VT via Nrf2-mediated antioxidation.

Atomic Imaging of Subsurface Interstitial Hydrogen and Insights into Surface Reactivity of Palladium Hydrides.

Resolving interstitial hydrogen atoms at the surfaces and interfaces is crucial for understanding the mechanical and physicochemical properties of metal hydrides. Although palladium (Pd) hydrides hold important applications in hydrogen storage and electrocatalysis, the atomic position of interstitial hydrogen at Pd hydride near surfaces still remains undetermined. We report the first direct imaging of subsurface hydrogen atoms absorbed in Pd nanoparticles by using differentiated and integrated differential phase contrast within an aberration-corrected scanning transmission electron microscope. In contrast to the well-established octahedral interstitial sites for hydrogen in the bulk, subsurface hydrogen atoms are directly identified to occupy the tetrahedral interstices. DFT calculations show that the amount and the occupation type of subsurface hydrogen atoms play an indispensable role in fine-tuning the electronic structure and associated chemical reactivity of the Pd surface.

Spatholobi Caulis dispensing granule reduces deep vein thrombus burden through antiinflammation via SIRT1 and Nrf2.

BACKGROUND: Deep vein thrombosis (DVT) is a kind of blood stasis syndrome. Spatholobi Caulis (SC) has been widely used for the treatment of blood stasis syndrome in China, but the underlying mechanism remains poorly understood. PURPOSE: The aim of present study was to investigate the anti-DVT mechanism of Spatholobi Caulis dispensing granule (SCDG). STUDY DESIGN/METHODS: A rat model of inferior vena cava (IVC) stenosis-induced DVT and a cell model of oxygen-glucose deprivation (OGD) were performed. Rats were orally administered with SCDG solution once daily for seven consecutive days. IVC stenosis-induced DVT was operated on the sixth day. Thrombi were harvested and weighed on the seventh day. Pathological changes were observed by hematoxylin-eosin (HE) staining. Tumor necrosis factor (TNF)-α and interleukin (IL)-1ß of serum were analyzed by enzyme-linked immunosorbent assay. C-reactive protein (CRP) was measured with turbidimetric immunoassay. Protein expressions in thrombosed IVCs and/or OGD-stimulated EA. hy926 cells were evaluated by western blot and/or immunofluorescence analyses. RESULTS: SCDG dramatically decreased thrombus weight. SCDG decreased tissue factor (TF) protein expression, inflammatory cells influxes in thrombosed vein wall and serum levels of inflammatory cytokines and CRP. Further, SCDG up-regulated Sirtuin 1 (SIRT1) protein expression and down-regulated acetylated-NF-κB p65 (Ace-p65) protein expression. Moreover, SCDG up-regulated nuclear factor-erythroid 2 related factor 2 (Nrf2) and heme oxygenase-1 (HO-1) protein expressions, and down-regulated phosphorylated-NF-κB p65 (p-p65) protein expression. In the OGD cell model, SCDG medicated serum decreased the protein expression of TF. SCDG medicated serum enhanced SIRT1 protein expression and reduced Ace-p65 nuclear protein expression. SCDG medicated serum promoted protein expressions of nuclear Nrf2 and total HO-1, and inhibited translocation of p65. Furthermore, inhibiting SIRT1 and Nrf2 reversed the protective effect of SCDG medicated serum on OGD-induced EA. hy926 cells. CONCLUSION: SCDG may prevent DVT through antiinflammation via SIRT1 and Nrf2.

Inferior vena cava stenosis-induced deep vein thrombosis is influenced by multiple factors in rats.

BACKGROUND: The pathogenesis of deep vein thrombosis (DVT) is incompletely understood, requiring reliable animal models. Inferior vena cava (IVC) stenosis model mimics human DVT. OBJECTIVE: To provide optimal conditions for establishing a rat model of IVC stenosis-induced DVT. METHODS: Effects of suture, and body weight, sex and side branches of rats on the IVC stenosis model were evaluated. 1 d after modeling, the weight and length of thrombosed IVCs and side branch distance were measured. Histopathological change and leukocytes influxes were observed by hematoxylin and eosin staining. Ly-6G-positive neutrophils were located by immunofluorescence. A multiple regression linear model was then built. RESULTS: IVCs stenosed with silk or monofilament sutures presented no difference in leukocyte influxes. Thrombus of 220-340 g rats was significantly heavier than that of 180-220 g rats. Although no statistic difference was found in thrombus weight between male and female rats weighing 180-260 g, males weighing 260-300 g formed larger thrombi than weight-matched females. Thrombus weight and length of rats except 180-220 g females was not impacted by side branch ligation and side branch distance. The regression model showed that sex and body weight were key factors affecting thrombus weight. CONCLUSIONS: Male and female rats weighing 220-260 g are more suitable for establishing a model of DVT induced by stenosing IVC with silk and without side branch ligation.

A statistical normalization method and differential expression analysis for RNA-seq data between different species.

BACKGROUND: High-throughput techniques bring novel tools and also statistical challenges to genomic research. Identifying genes with differential expression between different species is an effective way to discover evolutionarily conserved transcriptional responses. To remove systematic variation between different species for a fair comparison, normalization serves as a crucial pre-processing step that adjusts for the varying sample sequencing depths and other confounding technical effects. RESULTS: In this paper, we propose a scale based normalization (SCBN) method by taking into account the available knowledge of conserved orthologous genes and by using the hypothesis testing framework. Considering the different gene lengths and unmapped genes between different species, we formulate the problem from the perspective of hypothesis testing and search for the optimal scaling factor that minimizes the deviation between the empirical and nominal type I errors. CONCLUSIONS: Simulation studies show that the proposed method performs significantly better than the existing competitor in a wide range of settings. An RNA-seq dataset of different species is also analyzed and it coincides with the conclusion that the proposed method outperforms the existing method. For practical applications, we have also developed an R package named "SCBN", which is freely available at http://www.bioconductor.org/packages/devel/bioc/html/SCBN.html .

Stability of methods for differential expression analysis of RNA-seq data.

BACKGROUND: As RNA-seq becomes the assay of choice for measuring gene expression levels, differential expression analysis has received extensive attentions of researchers. To date, for the evaluation of DE methods, most attention has been paid on validity. Yet another important aspect of DE methods, stability, is overlooked and has not been studied to the best of our knowledge. RESULTS: In this study, we empirically show the need of assessing stability of DE methods and propose a stability metric, called Area Under the Correlation curve (AUCOR), that generates the perturbed datasets by a mixture distribution and combines the information of similarities between sets of selected features from these perturbed datasets and the original dataset. CONCLUSION: Empirical results support that AUCOR can effectively rank the DE methods in terms of stability for given RNA-seq datasets. In addition, we explore how biological or technical factors from experiments and data analysis affect the stability of DE methods. AUCOR is implemented in the open-source R package AUCOR, with source code freely available at https://github.com/linbingqing/stableDE .

Genome-Wide RNAi Screen Identify Melanoma-Associated Antigen Mageb3 Involved in X Chromosome Inactivation.

Xist (inactivated X chromosome specific transcript) is a prototype long noncoding RNA in charge of epigenetic silencing of one X chromosome in each female cell in mammals. In a genetic screen, we identify Mageb3 and its homologs Mageb1 and Mageb2 as genes functionally required for Xist-mediated gene silencing. Mageb1-3 are previously uncharacterized genes belonging to the MAGE (melanoma-associated antigen) gene family. Mageb1-3 are expressed in undifferentiated ES cells and early stages of in vitro differentiation, a critical time window of X chromosome inactivation. Mageb3 showed both cytoplasmic and nuclear localization without enrichment on the inactive X (Xi). Mageb3 interacted with Polycomb group ring finger 3 (Pcgf3), a RING finger protein involved in recruiting Polycomb activities onto Xi. Mageb3 overexpression stabilized Pcgf3 protein. Mageb1-3 gene knockout affected H3K27me3 enrichment and the spreading of gene silencing along Xi. These data suggested that Mageb3 might regulate the recruitment of the Polycomb complex onto Xi and subsequent H3K27me3 modification through Pcgf3. Moreover, the nucleolar enrichment of Mageb3 was diminished when nuclear matrix factor hnRNP U is overexpressed, implying the interaction between Mageb3 and nuclear matrix, which is another possible mechanism for Mageb3 to regulate X chromosome inactivation.

High-resolution RNA allelotyping along the inactive X chromosome: evidence of RNA polymerase III in regulating chromatin configuration.

We carried out padlock capture, a high-resolution RNA allelotyping method, to study X chromosome inactivation (XCI). We examined the gene reactivation pattern along the inactive X (Xi), after Xist (X-inactive specific transcript), a prototype long non-coding RNA essential for establishing X chromosome inactivation (XCI) in early embryos, is conditionally deleted from Xi in somatic cells (Xi∆Xist). We also monitored the behaviors of X-linked non-coding transcripts before and after XCI. In each mutant cell line, gene reactivation occurs to ~6% genes along Xi∆Xist in a recognizable pattern. Genes with upstream regions enriched for SINEs are prone to be reactivated. SINE is a class of retrotransposon transcribed by RNA polymerase III (Pol III). Intriguingly, a significant fraction of Pol III transcription from non-coding regions is not subjected to Xist-mediated transcriptional silencing. Pol III inhibition affects gene reactivation status along Xi∆Xist, alters chromatin configuration and interferes with the establishment XCI during in vitro differentiation of ES cells. These results suggest that Pol III transcription is involved in chromatin structure re-organization during the onset of XCI and functions as a general mechanism regulating chromatin configuration in mammalian cells.

LFCseq: a nonparametric approach for differential expression analysis of RNA-seq data.

BACKGROUND: With the advances in high-throughput DNA sequencing technologies, RNA-seq has rapidly emerged as a powerful tool for the quantitative analysis of gene expression and transcript variant discovery. In comparative experiments, differential expression analysis is commonly performed on RNA-seq data to identify genes/features that are differentially expressed between biological conditions. Most existing statistical methods for differential expression analysis are parametric and assume either Poisson distribution or negative binomial distribution on gene read counts. However, violation of distributional assumptions or a poor estimation of parameters often leads to unreliable results. RESULTS: In this paper, we introduce a new nonparametric approach called LFCseq that uses log fold changes as a differential expression test statistic. To test each gene for differential expression, LFCseq estimates a null probability distribution of count changes from a selected set of genes with similar expression strength. In contrast, the nonparametric NOISeq approach relies on a null distribution estimated from all genes within an experimental condition regardless of their expression levels. CONCLUSION: Through extensive simulation study and RNA-seq real data analysis, we demonstrate that the proposed approach could well rank the differentially expressed genes ahead of non-differentially expressed genes, thereby achieving a much improved overall performance for differential expression analysis.

Fixed and Random Effects Selection by REML and Pathwise Coordinate Optimization.

We propose a two-stage model selection procedure for the linear mixed-effects models. The procedure consists of two steps: First, penalized restricted log-likelihood is used to select the random effects, and this is done by adopting a Newton-type algorithm. Next, the penalized log-likelihood is used to select the fixed effects via pathwise coordinate optimization to improve the computation efficiency. We prove that our procedure has the oracle properties. Both simulation studies and a real data example are carried out to examine finite sample performance of the proposed fixed and random effects selection procedure. Supplementary materials including R code used in this article and proofs for the theorems are available online.