Modeling expression quantitative trait loci in data combining ethnic populations

<p>Abstract</p> <p>Background</p> <p>Combining data from different ethnic populations in a study can increase efficacy of methods designed to identify expression quantitative trait loci (eQTL) compared to analyzing each population independently. In such studies, however, the genetic diversity of minor allele frequencies among populations has rarely been taken into account. Due to the fact that allele frequency diversity and population-level expression differences are present in populations, a consensus regarding the optimal statistical approach for analysis of eQTL in data combining different populations remains inconclusive.</p> <p>Results</p> <p>In this report, we explored the applicability of a constrained two-way model to identify eQTL for combined ethnic data that might contain genetic diversity among ethnic populations. In addition, gene expression differences resulted from ethnic allele frequency diversity between populations were directly estimated and analyzed by the constrained two-way model. Through simulation, we investigated effects of genetic diversity on eQTL identification by examining gene expression data pooled from normal quantile transformation of each population. Using the constrained two-way model to reanalyze data from Caucasians and Asian individuals available from HapMap, a large number of eQTL were identified with similar genetic effects on the gene expression levels in these two populations. Furthermore, 19 single nucleotide polymorphisms with inter-population differences with respect to both genotype frequency and gene expression levels directed by genotypes were identified and reflected a clear distinction between Caucasians and Asian individuals.</p> <p>Conclusions</p> <p>This study illustrates the influence of minor allele frequencies on common eQTL identification using either separate or combined population data. Our findings are important for future eQTL studies in which different datasets are combined to increase the power of eQTL identification.</p

Nicotine replacement therapy for agitation and delirium management in the intensive care unit: a systematic review of the literature.

BACKGROUND: Active smokers are prevalent within the intensive care setting and place a significant burden on healthcare systems. Nicotine withdrawal due to forced abstinence on admission may contribute to increased agitation and delirium in this patient group. The aim of this systematic review was to determine whether management of nicotine withdrawal, with nicotine replacement therapy (NRT), reduces agitation and delirium in critically ill patients admitted to the intensive care unit (ICU). METHODS: The following sources were used in this review: MEDLINE, EMBASE, and CINAHL Plus databases. Included studies reported delirium or agitation outcomes in current smokers, where NRT was used as management of nicotine withdrawal, in the intensive care setting. Studies were included regardless of design or number of participants. Data were extracted on ICU classification; study design; population baseline characteristics; allocation and dose of NRT; agitation and delirium assessment methods; and the frequency of agitation, delirium, and psychotropic medication use. RESULTS: Six studies were included. NRT was mostly prescribed for smokers with heavier smoking histories. Three studies reported an association between increased agitation or delirium and NRT use; one study could not find any significant benefit or harm from NRT use; and two described a reduction of symptomatic nicotine withdrawal. A lack of consistent and validated assessment measures, combined with limitations in the quality of reported data, contribute to conflicting results. CONCLUSIONS: Current evidence for the use of NRT in agitation and delirium management in the ICU is inconclusive. An evaluation of risk versus benefit on an individual patient basis should be considered when prescribing NRT. Further studies that consider prognostic balance, adjust for confounders, and employ validated assessment tools are urgently needed

The Main Belt Comets and ice in the Solar System

We review the evidence for buried ice in the asteroid belt; specifically the questions around the so-called Main Belt Comets (MBCs). We summarise the evidence for water throughout the Solar System, and describe the various methods for detecting it, including remote sensing from ultraviolet to radio wavelengths. We review progress in the first decade of study of MBCs, including observations, modelling of ice survival, and discussion on their origins. We then look at which methods will likely be most effective for further progress, including the key challenge of direct detection of (escaping) water in these bodies

A review of RCTs in four medical journals to assess the use of imputation to overcome missing data in quality of life outcomes

Background: Randomised controlled trials (RCTs) are perceived as the gold-standard method for evaluating healthcare interventions, and increasingly include quality of life (QoL) measures. The observed results are susceptible to bias if a substantial proportion of outcome data are missing. The review aimed to determine whether imputation was used to deal with missing QoL outcomes. Methods: A random selection of 285 RCTs published during 2005/6 in the British Medical Journal, Lancet, New England Journal of Medicine and Journal of American Medical Association were identified. Results: QoL outcomes were reported in 61 (21%) trials. Six (10%) reported having no missing data, 20 (33%) reported ≤ 10% missing, eleven (18%) 11%–20% missing, and eleven (18%) reported >20% missing. Missingness was unclear in 13 (21%). Missing data were imputed in 19 (31%) of the 61 trials. Imputation was part of the primary analysis in 13 trials, but a sensitivity analysis in six. Last value carried forward was used in 12 trials and multiple imputation in two. Following imputation, the most common analysis method was analysis of covariance (10 trials). Conclusion: The majority of studies did not impute missing data and carried out a complete-case analysis. For those studies that did impute missing data, researchers tended to prefer simpler methods of imputation, despite more sophisticated methods being available.The Health Services Research Unit is funded by the Chief Scientist Office of the Scottish Government Health Directorate. Shona Fielding is also currently funded by the Chief Scientist Office on a Research Training Fellowship (CZF/1/31)

A review of RCTs in four medical journals to assess the use of imputation to overcome missing data in quality of life outcomes

Peer reviewedPublisher PD

NADPH oxidase-mediated redox signal contributes to lipoteichoic acid-induced MMP-9 upregulation in brain astrocytes

<p>Abstract</p> <p>Background</p> <p>Lipoteichoic acid (LTA) is a component of gram-positive bacterial cell walls and may be elevated in the cerebrospinal fluid of patients suffering from meningitis. Among matrix metalloproteinases (MMPs), MMP-9 has been observed in patients with brain inflammatory diseases and may contribute to the pathology of brain diseases. Moreover, several studies have suggested that increased oxidative stress is implicated in the pathogenesis of brain inflammation and injury. However, the molecular mechanisms underlying LTA-induced redox signal and MMP-9 expression in brain astrocytes remain unclear.</p> <p>Objective</p> <p>Herein we explored whether LTA-induced MMP-9 expression was mediated through redox signals in rat brain astrocytes (RBA-1 cells).</p> <p>Methods</p> <p>Upregulation of MMP-9 by LTA was evaluated by zymographic and RT-PCR analyses. Next, the MMP-9 regulatory pathways were investigated by pretreatment with pharmacological inhibitors or transfection with small interfering RNAs (siRNAs), Western blotting, and chromatin immunoprecipitation (ChIP)-PCR and promoter activity reporter assays. Moreover, we determined the cell functional changes by migration assay.</p> <p>Results</p> <p>These results showed that LTA induced MMP-9 expression via a PKC(α)-dependent pathway. We further demonstrated that PKCα stimulated p47^phox/NADPH oxidase 2 (Nox2)-dependent reactive oxygen species (ROS) generation and then activated the ATF2/AP-1 signals. The activated-ATF2 bound to the AP-1-binding site of MMP-9 promoter, and thereby turned on MMP-9 gene transcription. Additionally, the co-activator p300 also contributed to these responses. Functionally, LTA-induced MMP-9 expression enhanced astrocytic migration.</p> <p>Conclusion</p> <p>These results demonstrated that in RBA-1 cells, activation of ATF2/AP-1 by the PKC(α)-mediated Nox(2)/ROS signals is essential for upregulation of MMP-9 and cell migration enhanced by LTA.</p

Chemical characterization of extra layers at the interfaces in MOCVD InGaP/GaAs junctions by electron beam methods

Electron beam methods, such as cathodoluminescence (CL) that is based on an electron-probe microanalyser, and (200) dark field and high angle annular dark field (HAADF) in a scanning transmission electron microscope, are used to study the deterioration of interfaces in InGaP/GaAs system with the GaAs QW on top of InGaP. A CL emission peak different from that of the QW was detected. By using HAADF, it is found that the GaAs QW does not exist any longer, being replaced by extra interlayer(s) that are different from GaAs and InGaP because of atomic rearrangements at the interface. The nature and composition of the interlayer(s) are determined by HAADF. Such changes of the nominal GaAs QW can account for the emission observed by CL