Forecasting the Cross-Correlation of the CSST galaxy survey with the FAST HI Intensity Map

The cross-correlation of optical galaxies with the neutral hydrogen (HI) radiation intensity can enhance the signal-to-noise ratio (SNR) of the HI intensity measurement. In this paper, we investigate the cross-correlation of the galaxy samples obtained by the spectroscopic survey of the China Space Station Telescope (CSST) with the HI Intensity mapping (IM) survey of the Five-hundred-meter Aperture Spherical Telescope (FAST). Using the IllusitrisTNG simulation result at redshift $0.2 \sim 0.3$, we generate mock data of the CSST survey and a FAST L-band drift scan survey. The CSST spectroscopic survey can yield a sample of galaxies with a high comoving number density of 10^{-2} (\unit{Mpc}/h)^{-3} at $z \sim 0.3$. We cross-correlate the foreground-removed radio intensity with the CSST galaxies, including both the whole sample, and red and blue galaxy sub-samples separately. We find that in all cases the HI and optical galaxies are well correlated. The total HI abundance can be measured with a high precision from this correlation. A relative error of $\sim 0.6\%$ for $\Omega_{\rm HI}$ could be achieved at $z\sim 0.3$ for an overlapping survey area of 10000 \unit{deg}^2.Comment: 16 pages, 10 figure

Proteomic analysis of maize grain development using iTRAQ reveals temporal programs of diverse metabolic processes

Total proteins identified in maize grains (XLSX 745 kb

Plant Density and Nitrogen Supply Affect the Grain-Filling Parameters of Maize Kernels Located in Different Ear Positions

Although yield output of maize (Zea mays L.) has improved markedly over the last century, procedures for improving the grain-filling process remain elusive. Our aim in this study was to relate grain-filling variation in maize (including kernels in apical and middle positions in the ears) to plant density and nitrogen (N) application rate using a crossed experimental design. We also investigated changes in zeatin riboside (ZR), indole-3-acetic acid (IAA), abscisic acid (ABA), and gibberellic acid (GA) in the kernels during the grain-filling period. Two high-yield maize varieties cultivated extensively in China were field grown under normal (67,500 pl ha-1) and high (97,500 pl ha-1) densities, and supplied with low, normal and high (0, 180, and 360 kg N ha-1) concentrations of N. Kernel weight (KW), the maximum grain-filling rate (Gmax), the average grain-filling rate (Gave), and the kernel weight increment achieving Gmax (Wmax) were all significantly depressed under high density (HD) conditions, but increased N supply partially offset the losses. The apical kernels were more sensitive to density and N application rate than middle kernels. Correlation analysis indicated that plant density and N rate affected KW mainly by influencing the grain-filling rate. Variation in ZR, IAA, and ABA content tracked the variation in KW, but variation in GA content did not. Furthermore, the grain-filling parameters (closely related to TKW) had strong canonical correlation with the content of all hormones across the filling period and ZR content had the strongest relationship. Based on our study, high N supply is beneficial to optimize grain-filling parameters and improve KW of maize kernels under crowded condition

Indolic Uremic Solutes Enhance Procoagulant Activity of Red Blood Cells through Phosphatidylserine Exposure and Microparticle Release

Increased accumulation of indolic uremic solutes in the blood of uremic patients contributes to the risk of thrombotic events. Red blood cells (RBCs), the most abundant blood cells in circulation, may be a privileged target of these solutes. However, the effect of uremic solutes indoxyl sulfate (IS) and indole-3-acetic acid (IAA) on procoagulant activity (PCA) of erythrocyte is unclear. Here, RBCs from healthy adults were treated with IS and IAA (mean and maximal concentrations reported in uremic patients). Phosphatidylserine (PS) exposure of RBCs and their microparticles (MPs) release were labeled with Alexa Fluor 488-lactadherin and detected by flow cytometer. Cytosolic Ca2+ ([Ca2+]) with Fluo 3/AM was analyzed by flow cytometer. PCA was assessed by clotting time and purified coagulation complex assays. We found that PS exposure, MPs generation, and consequent PCA of RBCs at mean concentrations of IS and IAA enhanced and peaked in maximal uremic concentrations. Moreover, 128 nM lactadherin, a PS inhibitor, inhibited over 90% PCA of RBCs and RMPs. Eryptosis or damage, by indolic uremic solutes was due to, at least partially, the increase of cytosolic [Ca2+]. Our results suggest that RBC eryptosis in uremic solutes IS and IAA plays an important role in thrombus formation through releasing RMPs and exposing PS. Lactadherin acts as an efficient anticoagulant in this process

Negative Academic Emotion and Psychological Well-being in Chinese Rural-to-Urban Migrant Adolescents: Examining the Moderating Role of Cognitive Reappraisal

The study aimed to explore the relationship among negative academic emotions (e.g., anxiety, shame, anger, boredom, hopelessness, disappointment, and hatred), psychological well-being (including life vitality, health concern, altruism commitment, self-value, friendly relationship, and personal development), and cognitive reappraisal in rural-to-urban migrant adolescents in China. Specifically, it was hypothesized that the relationship between psychological well-being and negative academic emotions is moderated by cognitive reappraisal. A total of 311 migrant adolescents aged 14–20 years were selected, including 132 boys and 179 girls. Results of a regression analysis showed that cognitive reappraisal (positive) and negative academic emotions were significant predictors of psychological well-being. The interaction effect between cognitive reappraisal and negative academic emotion was also a significant predictor of psychological well-being. In the simple slope analysis the group with a below average cognitive reappraisal score the negative academic emotions were associated with lower psychological well-being, whereas in the group with above average cognitive reappraisal the effect of negative academic emotions on psychological well-being was not significant. However, for those with a cognitive reappraisal score of 1 standard deviation above the average, the effect of negative academic emotions on psychological well-being was not significant. These results suggest that cognitive reappraisal was a significant moderator in the relationship between negative academic emotion and psychological well-being

Multiomics and bioinformatics identify differentially expressed effectors in the brain of Toxoplasma gondii infected masked palm civet

IntroductionThe masked palm civet (Paguma larvata) serves as a reservoir in transmitting pathogens, such as Toxoplasma gondii, to humans. However, the pathogenesis of T. gondii infection in masked palm civets has not been explored. We studied the molecular changes in the brain tissue of masked palm civets chronically infected with T. gondii ME49.MethodsThe differentially expressed proteins in the brain tissue were investigated using iTRAQ and bioinformatics.ResultsA total of 268 differential proteins were identified, of which 111 were upregulated and 157 were downregulated. KEGG analysis identified pathways including PI3K-Akt signaling pathway, proteoglycans in cancer, carbon metabolism, T-cell receptor signaling pathway. Combing transcriptomic and proteomics data, we identified 24 genes that were differentially expressed on both mRNA and protein levels. The top four upregulated proteins were REEP3, REEP4, TEP1, and EEPD1, which was confirmed by western blot and immunohistochemistry. KEGG analysis of these 24 genes identified signaling cascades that were associated with small cell lung cancer, breast cancer, Toll-like receptor signaling pathway, Wnt signaling pathways among others. To understand the mechanism of the observed alteration, we conducted immune infiltration analysis using TIMER databases which identified immune cells that are associated with the upregulation of these proteins. Protein network analysis identified 44 proteins that were in close relation to all four proteins. These proteins were significantly enriched in immunoregulation and cancer pathways including PI3K-Akt signaling pathway, Notch signaling pathway, chemokine signaling pathway, cell cycle, breast cancer, and prostate cancer. Bioinformatics utilizing two cancer databases (TCGA and GEPIA) revealed that the four genes were upregulated in many cancer types including glioblastoma (GBM). In addition, higher expression of REEP3 and EEPD1 was associated with better prognosis, while higher expression of REEP4 and TEP1 was associated with poor prognosis in GBM patients.DiscussionWe identified the differentially expressed genes in the brain of T. gondii infected masked palm civets. These genes were associated with various cellular signaling pathways including those that are immune- and cancer-related

The Genomes of Oryza sativa: A History of Duplications

We report improved whole-genome shotgun sequences for the genomes of indica and japonica rice, both with multimegabase contiguity, or almost 1,000-fold improvement over the drafts of 2002. Tested against a nonredundant collection of 19,079 full-length cDNAs, 97.7% of the genes are aligned, without fragmentation, to the mapped super-scaffolds of one or the other genome. We introduce a gene identification procedure for plants that does not rely on similarity to known genes to remove erroneous predictions resulting from transposable elements. Using the available EST data to adjust for residual errors in the predictions, the estimated gene count is at least 38,000–40,000. Only 2%–3% of the genes are unique to any one subspecies, comparable to the amount of sequence that might still be missing. Despite this lack of variation in gene content, there is enormous variation in the intergenic regions. At least a quarter of the two sequences could not be aligned, and where they could be aligned, single nucleotide polymorphism (SNP) rates varied from as little as 3.0 SNP/kb in the coding regions to 27.6 SNP/kb in the transposable elements. A more inclusive new approach for analyzing duplication history is introduced here. It reveals an ancient whole-genome duplication, a recent segmental duplication on Chromosomes 11 and 12, and massive ongoing individual gene duplications. We find 18 distinct pairs of duplicated segments that cover 65.7% of the genome; 17 of these pairs date back to a common time before the divergence of the grasses. More important, ongoing individual gene duplications provide a never-ending source of raw material for gene genesis and are major contributors to the differences between members of the grass family

Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data