Confidence bands for cumulative incidence curves under the additive risk model

In the context of competing risks, the cumulative incidence function is often used to summarize the cause-specific failure-time data. As an alternative to the proportional hazards model, the additive risk model is used to investigate covariate effects by specifying that the subject-specific hazard function is the sum of a baseline hazard function and a regression function of covariates. Based on such a formulation, we present an approach to constructing simultaneous confidence intervals for the cause-specific cumulative incidence function of patients with given risk factors. A melanoma data set is used for the purpose of illustration.     

SRFR1 Negatively Regulates Plant NB-LRR Resistance Protein Accumulation to Prevent Autoimmunity

Plant defense responses need to be tightly regulated to prevent auto-immunity, which is detrimental to growth and development. To identify negative regulators of Resistance (R) protein-mediated resistance, we screened for mutants with constitutive defense responses in the npr1-1 background. Map-based cloning revealed that one of the mutant genes encodes a conserved TPR domain-containing protein previously known as SRFR1 (SUPPRESSOR OF rps4-RLD). The constitutive defense responses in the srfr1 mutants in Col-0 background are suppressed by mutations in SNC1, which encodes a TIR-NB-LRR (Toll Interleukin1 Receptor-Nucleotide Binding-Leu-Rich Repeat) R protein. Yeast two-hybrid screens identified SGT1a and SGT1b as interacting proteins of SRFR1. The interactions between SGT1 and SRFR1 were further confirmed by co-immunoprecipitation analysis. In srfr1 mutants, levels of multiple NB-LRR R proteins including SNC1, RPS2 and RPS4 are increased. Increased accumulation of SNC1 is also observed in the sgt1b mutant. Our data suggest that SRFR1 functions together with SGT1 to negatively regulate R protein accumulation, which is required for preventing auto-activation of plant immunity.     

Identification and isolation of anaerobic, syntrophic phthalate isomer-degrading microbes from methanogenic sludges treating wastewater from terephthalate manufacturing

The microbial populations responsible for anaerobic degradation of phthalate isomers were investigated by enrichment and isolation of those microbes from anaerobic sludge treating wastewater from the manufacturing of terephthalic acid. Primary enrichments were made with each of three phthalate isomers (ortho-, iso-, and terephthalate) as the sole energy source at 37 degrees C with two sources of anaerobic sludge (both had been used to treat wastewater containing high concentrations of phthalate isomers) as the inoculum. Six methanogenic enrichment cultures were obtained which not only degraded the isomer used for the enrichment but also had the potential to degrade part of other phthalate isomers as well as benzoate with concomitant production of methane, presumably involving strictly syntrophic substrate degradation. Our 16S rRNA gene-cloning analysis combined with fluorescence in situ hybridization revealed that the predominant bacteria in the enrichment cultures were affiliated with a recently recognized non-sulfate-reducing subcluster (subcluster Ih) in the group 'Desulfotomaculum lineage I' or a clone cluster (group TA) in the class delta-PROTEOBACTERIA: Several attempts were made to isolate these microbes, resulting in the isolation of a terephthalate-degrading bacterium, designated strain JT, in pure culture. A coculture of the strain with the hydrogenotrophic methanogen Methanospirillum hungatei converted terephthalate to acetate and methane within 3 months of incubation, whereas strain JT could not degrade terephthalate in pure culture. During the degradation of terephthalate, a small amount of benzoate was transiently accumulated as an intermediate, indicative of decarboxylation of terephthalate to benzoate as the initial step of the degradation. 16S rRNA gene sequence analysis revealed that the strain was a member of subcluster Ih of the group 'Desulfotomaculum lineage I', but it was only distantly related to other known species.     

Continuum simulations of acetylcholine diffusion with reaction-determined boundaries in neuromuscular junction models

The reaction-diffusion system of the neuromuscular junction has been modeled in 3D using the finite element package FEtk. The numerical solution of the dynamics of acetylcholine with the detailed reaction processes of acetylcholinesterases and nicotinic acetylcholine receptors has been discussed with the reaction-determined boundary conditions. The simulation results describe the detailed acetylcholine hydrolysis process, and reveal the time-dependent interconversion of the closed and open states of the acetylcholine receptors as well as the percentages of unliganded/monoliganded/diliganded states during the neuro-transmission. The finite element method has demonstrated its flexibility and robustness in modeling large biological systems.     

Determinants of the interaction of the spinal muscular atrophy disease protein SMN with the dimethylarginine-modified box H/ACA small nucleolar ribonucleoprotein GAR1

Deletion or mutation of the SMN1 (survival of motor neurons) gene causes the common, fatal neuromuscular disease spinal muscular atrophy. The SMN protein is important in small nuclear ribonucleoprotein (snRNP) assembly and interacts with snRNP proteins via arginine/glycine-rich domains. Recently, SMN was also found to interact with core protein components of the two major families of small nucleolar RNPs, fibrillarin and GAR1, suggesting that SMN may also function in the assembly of small nucleolar RNPs. Here we present results that indicate that the interaction of SMN with GAR1 is mediated by the Tudor domain of SMN. Single point mutations within the Tudor domain, including a spinal muscular atrophy patient mutation, impair the interaction of SMN with GAR1. Furthermore, we find that either of the two arginine/glycine-rich domains of GAR1 can provide for interaction with SMN, but removal of both results in loss of the interaction. Finally, we have found that unlike the interaction of SMN with the Sm snRNP proteins, interaction with GAR1 and fibrillarin is not enhanced by arginine dimethylation. Our results argue against post-translational arginine dimethylation as a general requirement for SMN recognition of proteins bearing arginine/glycine-rich domains.     

Single‐Ion Conducting Electrolyte Based on Electrospun Nanofibers for High‐Performance Lithium Batteries

Herein, a novel electrospun single‐ion conducting polymer electrolyte (SIPE) composed of nanoscale mixed poly(vinylidene fluoride‐co‐hexafluoropropylene) (PVDF‐HFP) and lithium poly(4,4′‐diaminodiphenylsulfone, bis(4‐carbonyl benzene sulfonyl)imide) (LiPSI) is reported, which simultaneously overcomes the drawbacks of the polyolefin‐based separator (low porosity and poor electrolyte wettability and thermal dimensional stability) and the LiPF₆ salt (poor thermal stability and moisture sensitivity). The electrospun nanofiber membrane (es‐PVPSI) has high porosity and appropriate mechanical strength. The fully aromatic polyamide backbone enables high thermal dimensional stability of es‐PVPSI membrane even at 300 °C, while the high polarity and high porosity ensures fast electrolyte wetting. Impregnation of the membrane with the ethylene carbonate (EC)/dimethyl carbonate (DMC) (v:v = 1:1) solvent mixture yields a SIPE offering wide electrochemical stability, good ionic conductivity, and high lithium‐ion transference number. Based on the above‐mentioned merits, Li/LiFePO₄ cells using such a SIPE exhibit excellent rate capacity and outstanding electrochemical stability for 1000 cycles at least, indicating that such an electrolyte can replace the conventional liquid electrolyte–polyolefin combination in lithium ion batteries (LIBs). In addition, the long‐term stripping–plating cycling test coupled with scanning electron microscope (SEM) images of lithium foil clearly confirms that the es‐PVPSI membrane is capable of suppressing lithium dendrite growth, which is fundamental for its use in high‐energy Li metal batteries.     

Effects of high temperature coupled with high light on the balance between photooxidation and photoprotection in the sun-exposed peel of apple

The sun-exposed peel of 'Gala' apple with or without sunburn was compared in terms of photooxidation and photoprotection, and a controlled experiment was conducted to probe the initial responses of PSII to high light and high temperature. The content of carotenoids, lutein and xanthophylls on a chlorophyll basis was higher in the sunburned peel although they were lower expressed on a peel area basis. Significant loss of beta-carotene and neoxanthin was observed relative to chlorophylls in the sunburned peel. O(2) evolution rates and the activity of key enzymes in the Calvin cycle were lower in the sunburned peel, but the activity of these enzymes decreased to a lesser extent than the O(2) evolution rates. The activity of antioxidant enzymes in the ascorbate-glutathione cycle and the level of total ascorbate, total glutathione, and reduced glutathione were higher in the sunburned peel. However, the sunburned peel had higher H(2)O(2) and malondialdehyde contents. Fruit peels treated with high temperature (45 degrees C) alone showed a clear "K" step in their chlorophyll fluorescence transients whereas high temperature coupled with high light (1,600 mumol m(-2) s(-1)) led to the disappearance of the "K" step and a further decrease in F (V)/F (M) (similar to what was observed in the sunburned peel). We conclude that high temperature coupled with high light damages the PSII complexes at both the donor and acceptor sides. Although both the xanthophyll cycle and the antioxidant system are up-regulated in response to the photooxidative stress, this up-regulation does not provide enough protection against the photooxidation.