A Comparison of the TempO-Seq S1500+ Platform to RNA-Seq and Microarray Using Rat Liver Mode of Action Samples

The TempO-SeqTM platform allows for targeted transcriptomic analysis and is currently used by many groups to perform high-throughput gene expression analysis. Herein we performed a comparison of gene expression characteristics measured using 45 purified RNA samples from the livers of rats exposed to chemicals that fall into one of five modes of action (MOAs). These samples have been previously evaluated using AffymetrixTM rat genome 230 2.0 microarrays and Illumina® whole transcriptome RNA-Seq. Comparison of these data with TempO-Seq analysis using the rat S1500+ beta gene set identified clear differences in the platforms related to signal to noise, root mean squared error, and/or sources of variability. Microarray and TempO-Seq captured the most variability in terms of MOA and chemical treatment whereas RNA-Seq had higher noise and larger differences between samples within a MOA. However, analysis of the data by hierarchical clustering, gene subnetwork connectivity and biological process representation of MOA-varying genes revealed that the samples clearly grouped by treatment as opposed to gene expression platform. Overall these findings demonstrate that the results from the TempO-Seq platform are consistent with findings on other more established approaches for measuring the genome-wide transcriptome

Molecular simulations of the synthesis of periodic mesoporous silica phases at high surfactant concentrations

Molecular dynamics simulations of a coarse-grained model are used to study the formation mechanism of periodic mesoporous silica over a wide range of cationic surfactant concentrations. This follows up on an earlier study of systems with low surfactant concentrations. We started by studying the phase diagram of the surfactant-water system and found that our model shows good qualitative agreement with experiments with respect to the surfactant concentrations where various phases appear. We then considered the impact of silicate species upon the morphologies formed. We have found that even in concentrated surfactant systems --in the concentration range where pure surfactant solutions yield a liquid crystal phase -- the liquid-crystal templating mechanism is not viable because the preformed liquid crystal collapses as silica monomers are added into the solution. Upon the addition of silica dimers, a new phase-separated hexagonal array is formed. The preformed liquid crystals were found to be unstable in the presence of monomeric silicates. In addition, the silica dimer is found to be essential for mesoscale ordering at both low and high surfactant concentrations. Our results support the view that a cooperative interaction of anionic silica oligomers and cationic surfactants determines the mesostructure formation in the M41S family of materials.publishe

Infectious Complications of Ventricular Assist Device Use in Children in the US: Data from the Pediatric Interagency Registry for Mechanical Circulatory Support (Pedimacs)

Background Infections are frequent in pediatric ventricular assist device (VAD) patients. In this study we aimed to describe infections in durable VAD patients reported to Pedimacs. Methods Durable VAD data from the Pedimacs registry (September 19, 2012 to December 31, 2015) were analyzed. Infections were described with standard descriptive statistics, Kaplan–Meier analysis and competing outcomes analysis. Results There were 248 implants in 222 patients, with a mean age and a median follow-up of 11 ± 6.4 years and 2.4 patient-months (<1 day to 2.6 years), respectively. Device types were pulsatile flow (PF) in 91 (41%) patients and continuous flow (CF) in 131 (59%) patients. PF patients were younger (4 ± 4 vs 14 ± 4 years; p < 0.0001) and were more likely to have congenital heart disease (25% vs 12%; p = 0.03), prior surgery (53% vs 26%; p < 0.0001) and prior extracorporeal membrane oxygenation (24% vs 7%; p = 0.0003). Infection accounted for 17% (96 of 564) of the reported adverse events (AEs). A non-device infection was most common (51%), followed by sepsis (24%), external pump component infection (20%) and internal pump component infection (5%). Most infections were bacterial (73%) and required intravenous therapy only (77%). The risk of infection in the constant phase was higher in patients with a history of prior infection and in patients with a history of a non-infectious major AEs. Survival was lower after infection only in CF patients (p = 0.008). Conclusions Infection was the most common AE after pediatric VAD implantation. Non-device infections were most common. The best predictor of a future infection was a past infection. CF patients have higher risk of death after an infection

Multiscale model for the templated synthesis of mesoporous silica: the essential role of silica oligomers

A detailed theoretical understanding of the synthesis mechanism of periodic mesoporous silica has not yet been achieved. We present results of a multiscale simulation strategy that, for the first time, describes the molecular-level processes behind the formation of silica/surfactant mesophases in the synthesis of templated MCM-41 materials. The parameters of a new coarse-grained explicit-solvent model for the synthesis solution are calibrated with reference to a detailed atomistic model, which itself is based on quantum mechanical calculations. This approach allows us to reach the necessary time and length scales to explicitly simulate the spontaneous formation of mesophase structures while maintaining a level of realism that allows for direct comparison with experimental systems. Our model shows that silica oligomers are a necessary component in the formation of hexagonal liquid crystals from low-concentration surfactant solutions. Because they are multiply charged, silica oligomers are able to bridge adjacent micelles, thus allowing them to overcome their mutual repulsion and form aggregates. This leads the system to phase separate into a dilute solution and a silica/surfactant-rich mesophase, which leads to MCM-41 formation. Before extensive silica condensation takes place, the mesophase structure can be controlled by manipulation of the synthesis conditions. Our modeling results are in close agreement with experimental observations and strongly support a cooperative mechanism for synthesis of this class of materials. This work paves the way for tailored design of nanoporous materials using computational models

Transactivation of a DR-1 PPRE by a human constitutive androstane receptor variant expressed from internal protein translation start sites

Downstream in-frame start codons produce amino-terminal-truncated human constitutive androstane receptor protein isoforms (ΔNCARs). The ΔNCARs are expressed in liver and in vitro cell systems following translation from in-frame methionine AUG start codons at positions 76, 80, 125, 128, 168 and 265 within the full-length CAR mRNA. The resulting CAR proteins lack the N-terminal DNA-binding domain (DBD) of the receptor, yielding ΔNCAR variants with unique biological function. Although the ΔNCARs maintain full retinoid X receptor alpha (RXRα) heterodimerization capacity, the ΔNCARs are inactive on classical CAR-inducible direct repeat (DR)-4 elements, yet efficiently transactivate a DR-1 element derived from the endogenous PPAR-inducible acyl-CoA oxidase gene promoter. RXRα heterodimerization with CAR1, CAR76 and CAR80 isoforms is necessary for the DR-1 PPRE activation, a function that exhibits absolute dependence on both the respective RXRα DBD and CAR activation (AF)-2 domains, but not the AF-1 or AF-2 domain of RXRα, nor CAR's DBD. A new model of CAR DBD-independent transactivation is proposed, such that in the context of a DR-1 peroxisome proliferator-activated response element, only the RXRα portion of the CAR-RXRα heterodimer binds directly to DNA, with the AF-2 domain of tethered CAR mediating transcriptional activation of the receptor complex

Interprofessional communication with hospitalist and consultant physicians in general internal medicine : a qualitative study

This study helps to improve our understanding of the collaborative environment in GIM, comparing the communication styles and strategies of hospitalist and consultant physicians, as well as the experiences of providers working with them. The implications of this research are globally important for understanding how to create opportunities for physicians and their colleagues to meaningfully and consistently participate in interprofessional communication which has been shown to improve patient, provider, and organizational outcomes

Epigenome-Wide DNA Methylation and Pesticide Use in the Agricultural Lung Health Study

Using family-wise error rate (p<9×10-8) or false-discovery rate (FDR<0.05), we identified 162 differentially methylated CpGs across 8 of 9 currently marketed active ingredients (acetochlor, atrazine, dicamba, glyphosate, malathion, metolachlor, mesotrione, and picloram) and one banned organochlorine (heptachlor). Differentially methylated CpGs were unique to each active ingredient, and a dose-response relationship with lifetime days of use was observed for most. Significant CpGs were enriched for transcription motifs and 28% of CpGs were associated with whole blood cis-gene expression, supporting functional effects of findings. We corroborated a previously reported association between dichlorodiphenyltrichloroethane (banned in the United States in 1972) and epigenetic age acceleration