Analysis of multivariate recurrent event data with time‐dependent covariates and informative censoring

Multivariate recurrent event data are usually encountered in many clinical and longitudinal studies in which each study subject may experience multiple recurrent events. For the analysis of such data, most existing approaches have been proposed under the assumption that the censoring times are noninformative, which may not be true especially when the observation of recurrent events is terminated by a failure event. In this article, we consider regression analysis of multivariate recurrent event data with both time‐dependent and time‐independent covariates where the censoring times and the recurrent event process are allowed to be correlated via a frailty. The proposed joint model is flexible where both the distributions of censoring and frailty variables are left unspecified. We propose a pairwise pseudolikelihood approach and an estimating equation‐based approach for estimating coefficients of time‐dependent and time‐independent covariates, respectively. The large sample properties of the proposed estimates are established, while the finite‐sample properties are demonstrated by simulation studies. The proposed methods are applied to the analysis of a set of bivariate recurrent event data from a study of platelet transfusion reactions.     

Cellulose microfibril angle variation in Picea crassifolia tree rings improves climate signals on the Tibetan plateau

Microfibril angle (MFA) is an important factor in determining the mechanical properties of individual cells and wood as a whole. While some studies have described the variation of MFA within trees, little work has been done on the extent to which MFA is influenced by climate, despite it being known to respond to climatic events. Year-to-year variation in MFA and ring width was measured at high resolution by SilviScan-3^? on 30 dated Picea crassifolia trees growing in the northeastern Tibetan plateau. The climate signals registered in MFA and ring width were analyzed using dendroclimatological methods. The response function of MFA accounted for 67% of total variance, of which 60% was explained by climate elements. The response function of ring width explained 57% total variance, 37% of which was explained by climate variables. MFA significantly responded to July–August temperatures, and to precipitation in March, May and September. Over the period 1987–2009 temperatures generally increase and appeared to have a greater influence on MFA. A decrease in the strength of the relationship between MFA and ring width over the period 1987–2009 was also observed. MFA offers the potential to build robust climate proxies. The strong climate sensitivity of MFA to increasing temperature or the observed changes in the MFA–ring width relationship may contribute to resolving the “divergence problem” in temperature reconstructions. As far as we are aware, this study is the first to show a strong climate response in MFA and suggests that it might be a useful climate proxy.     

Effect of two selenium sources on hepatocarcinogenesis and several angiogenic cytokines in diethylnitrosamine-induced hepatocarcinoma rats

This experiment was designed to compare the effect of two selenium sources at the dosage of therapeutic level on hepatocarcinogenesis and angiogenic cytokines in DEN-induced hepatocarcinoma rats to further approach their possible anticancer's mechanism. One hundred and seventy-eight Sprague-Dawley (SD) rats (average weight being 100–120 g) were randomly divided into 5 groups (I–V). Animals in group I, group II and group III served as the negative control, sodium selenite control (SS) and positive controls respectively, and received 0.1, 3.0, and 0.1 mg/kg selenium from sodium selenite supplemented diets during the whole experimental time. Rats in group IV and group V were fed with selenium from selenium-enriched malt (SEM) and sodium selenite (SS) supplemented diets (3 mg/kg respectively). To balance the nutritional content among each group, normal malt which was not treated with selenium was added into the diets of the challenge groups. The nutrition contents, except the selenium of the diet in each group, were similar and in accordance with NRC standards. Rats in groups III–V were treated by aqueous diethylnitrosamine solution (100 mg/L) at the dosage of 10 mg/kg body weight every day for 16 weeks to induce hepatocarcinoma, and drank sterilized water for an additional two weeks. Rats in group I and group II drank sterilized water throughout the experiment. At 4th, 8th, 12th, 16th week, five rats in each group were then sacrificed by cervical decapitation. At the termination of the study, at 18th week, the surplus rats were sacrificed by cervical decapitation. Feed was withheld from the rats for 12 h before sampling. The number of hepatoma nodules in liver and mortality of rats were calculated. The values of the following items, including α-fetoprotein (AFP), gamma-glutamyltranspeptidase (GGT), tumor necrosis factor-α (TNF-α), insulin-like growth factors-II (IGF-II), nitric oxide (NO) and total nitric oxide synthase (T-NOS) in plasma were determined. At the same time, the positive numbers of vascular endothelial growth factor (VEGF) and protein kinase C-α (PKCα) staining cells in tumor tissue were analyzed by immunohistochemistry using the Envision two step methods with a kit. The results indicated that SEM could significantly decrease the mortality of rats and the number of hepatoma nodules, values of GGT and AFP, and the levels of IGF-II, NO and NOS and lessen the positive numbers of VEGF and PKCα staining cells in tumor tissue. Moreover, SEM could increase the levels of TNF-α in the initiated time of hepatocarcinogenesis, whereas, decrease the levels of TNF-α in the progressive time of hepatocarcinogenesis. SS could only significantly inhibit the positive numbers of PKCα staining cells in tumor tissue, decrease the levels of GGT, AFP and TNF-α at minority sampling times, and increase the levels of NO. In conclusion, SEM could reduce the mortality. It might be related to deaden significantly the lesion of liver, delay the cause of hepatocarcinogenesis, and inhibit the progress of angiogenesis to increase the livability of DEN-induced hepatocarcinoma rats. SS at the same therapeutic dosage had less effect on the hepatocarcinogenesis by inhibiting angiogenesis and relative cytokines to some extent.     

Purification and Structural Characterization of Dendrobium officinale Polysaccharides and Its Activities

In this study, Dendrobium officinale polysaccharide (named DOPS-1) was isolated from the stems of Dendrobium officinale by hot-water extraction and purified by using Sephadex G-150 column chromatography. The structural characterization, antioxidant and cytotoxic activity were carried out. Based on the results of HPLC, GC, Congo red experiment, together with periodate oxidation, Smith degradation, SEM, FT-IR, and NMR spectral analysis, it expressed that DOPS-1 was largely composed of mannose, glucose and galacturonic acid in a molar ratio of 3.2 : 1.3 : 1. The molecular weight of DOPS-1 was 1530 kDa and the main chain was composed of (1→4)-β-D-Glcp, (1→4)-β-D-Manp and 2-O-acetyl-(1→4)-β-D-Manp. The measurement results of antioxidant activity showed that DOPS-1 had the strong scavenging activities on hydroxyl radicals, DPPH radicals and superoxide radicals and the high reducing ability in vitro. Moreover, DOPS-1 was cytotoxic to all three human cancer cells of MDA-MB-231, A549 and HepG2.     

Molecular mechanisms of <Emphasis Type="Italic">Bombyx batryticatus</Emphasis> ethanol extract inducing gastric cancer SGC-7901 cells apoptosis

Bombyx batryticatus is a traditional Chinese medicine. To understand apoptotic effect of B. batryticatus ethanol extract (BBE), we investigated the role of BBE in inducing apoptosis of human gastric cancer cells SGC-7901. Cells treated with BBE and apoptosis was assessed by methyl thiazolyl tetrazolium (MTT) assay, morphological changes, DNA fragmentation and flow cytometry assays. The expression of Bcl-2, Bax and P21 were evaluated by western blot analysis and real time polymerase chain reaction. MTT assay showed that the cytotoxicity of BBE extract on SGC-7901 cells was correlated with treatment time and concentration. After treatment with 6 mg/mL of BBE the microscopy showed that, the majority of SGC-7901 cells were obviously reduced, distorted and grew slowly. Annexin-V/propidium iodide double-staining assay emerge the early apoptosis and the late apoptosis after treatment with different times by laser confocal fluorescence microscopy and flow cytometer. Cell cycle analysis of SGC 79 cells showed that BBE induced cell cycle arrest in the G1 and G2 phases. DNA fragmentation indicated the trend of BBE inducing apoptosis on SGC-7901 cells. The qRT-PCR and western blot analysis indicated that the mRNA and protein expressions of Bax and P21 were significantly up-regulated whereas that of Bc1-2 was down-regulated after treatment with BBE for 24 h. Our results revealed a correlation between gene regulation and BBE-induced apoptosis, which might indicate the potential of BBE in cancer therapy.     

Protective Effects of Lactobacillus plantarum CCFM8610 against Chronic Cadmium Toxicity in Mice Indicate Routes of Protection besides Intestinal Sequestration

Our previous study confirmed the ability of Lactobacillus plantarum CCFM8610 to protect against acute cadmium (Cd) toxicity in mice. This study was designed to evaluate the protective effects of CCFM8610 against chronic Cd toxicity in mice and to gain insights into the protection mode of this strain. Experimental mice were divided into two groups and exposed to Cd for 8 weeks via drinking water or intraperitoneal injection. Both groups were further divided into four subgroups, control, Cd only, CCFM8610 only, and Cd plus CCFM8610. Levels of Cd were measured in the feces, liver, and kidneys, and alterations of several biomarkers of Cd toxicity were noted. The results showed that when Cd was introduced orally, cotreatment with Cd and CCFM8610 effectively decreased intestinal Cd absorption, reduced Cd accumulation in tissue, alleviated tissue oxidative stress, reversed hepatic and renal damage, and ameliorated the corresponding histopathological changes. When Cd was introduced intraperitoneally, administration of CCFM8610 did not have an impact on tissue Cd accumulation or reverse the activities of antioxidant enzymes. However, CCFM8610 still offered protection against oxidative stress and reversed the alterations of Cd toxicity biomarkers and tissue histopathology. These results suggest that CCFM8610 is effective against chronic cadmium toxicity in mice. Besides intestinal Cd sequestration, CCFM8610 treatment offers direct protection against Cd-induced oxidative stress. We also provide evidence that the latter is unlikely to be mediated via protection against Cd-induced alteration of antioxidant enzyme activities.     

High-quality genome assembly of Huazhan and Tianfeng,the parents of an elite rice hybrid Tian-you-hua-zhan

High-quality rice reference genomes have accelerated the comprehensive identification of genome-wide variations and research on functional genomics and breeding. Tian-you-hua-zhan has been a leading hybrid in China over the past decade. Here, de novo genome assembly strategy optimization for the rice indica lines Huazhan (HZ) and Tianfeng (TF), including sequencing platforms, assembly pipelines and sequence depth, was carried out. The PacBio and Nanopore platforms for long-read sequencing were utilized, with the Canu, wtdbg2, SMARTdenovo, Flye, Canu-wtdbg2, Canu-SMARTdenovo and Canu-Flye assemblers. The combination of PacBio and Canu was optimal, considering the contig N50 length, contig number, assembled genome size and polishing process. The assembled contigs were scaffolded with Hi-C data, resulting in two “golden quality” rice reference genomes, and evaluated using the scaffold N50, BUSCO, and LTR assembly index. Furthermore, 42,625 and 41,815 non-transposable element genes were annotated for HZ and TF, respectively. Based on our assembly of HZ and TF, as well as Zhenshan97, Minghui63, Shuhui498 and 9311, comprehensive variations were identified using Nipponbare as a reference. The de novo assembly strategy for rice we optimized and the “golden quality” rice genomes we produced for HZ and TF will benefit rice genomics and breeding research, especially with respect to uncovering the genomic basis of the elite traits of HZ and TF.