PPARγ2 Pro12Ala polymorphism was associated with favorable cardiometabolic risk profile in HIV/HCV coinfected patients: a cross-sectional study

Targeted plasma proteomics reveals upregulation of distinct inflammatory pathways in people living with HIV

Despite antiretroviral therapy (ART), people living with HIV (PLHIV) display persistent inflammation leading to non-AIDS-related co-morbidities. To better understand underlying mechanisms, we compared targeted plasma inflammatory protein concentration (n = 92) between a cohort of 192 virally suppressed PLHIV, who were followed-up for five years, and 416 healthy controls (HC). Findings were validated in an independent cohort of 649 virally suppressed PLHIV and 98 HC. Compared to HC, PLHIV exhibited distinctively upregulated inflammatory proteins, including mucosal defense chemokines, CCR5 and CXCR3 ligands, and growth factors. Unsupervised clustering of inflammatory proteins clearly differentiated PLHIV with low (n = 123) and high inflammation (n = 65), the latter having a 3.4 relative risk (95% confidence interval 1.2-9.8) to develop malignancies and trend for cardiovascular events during a 5-year follow-up. The best protein predictors discriminating the two inflammatory endotypes were PD-L1, VEGFA, LAP TGF β-1, and TNFRSF9. Our data provide insights into co-morbidities associated inflammatory changes in PLHIV on long-term ART.

Biomarker Signatures of Quality for Engineering Nasal Chondrocyte-Derived Cartilage

The definition of quality controls for cell therapy and engineered product manufacturing processes is critical for safe, effective, and standardized clinical implementation. Using the example context of cartilage grafts engineered from autologous nasal chondrocytes, currently used for articular cartilage repair in a phase II clinical trial, we outlined how gene expression patterns and generalized linear models can be introduced to define molecular signatures of identity, purity, and potency. We first verified that cells from the biopsied nasal cartilage can be contaminated by cells from a neighboring tissue, namely perichondrial cells, and discovered that they cannot deposit cartilaginous matrix. Differential analysis of gene expression enabled the definition of identity markers for the two cell populations, which were predictive of purity in mixed cultures. Specific patterns of expression of the same genes were significantly correlated with cell potency, defined as the capacity to generate tissues with histological and biochemical features of hyaline cartilage. The outlined approach can now be considered for implementation in a good manufacturing practice setting, and offers a paradigm for other regenerative cellular therapies.

Sample size calculations for skewed distributions

Background

Sample size calculations should correspond to the intended method of analysis. Nevertheless, for non-normal distributions, they are often done on the basis of normal approximations, even when the data are to be analysed using generalized linear models (GLMs).

Methods

For the case of comparison of two means, we use GLM theory to derive sample size formulae, with particular cases being the negative binomial, Poisson, binomial, and gamma families. By simulation we estimate the performance of normal approximations, which, via the identity link, are special cases of our approach, and for common link functions such as the log. The negative binomial and gamma scenarios are motivated by examples in hookworm vaccine trials and insecticide-treated materials, respectively.

Results

Calculations on the link function (log) scale work well for the negative binomial and gamma scenarios examined and are often superior to the normal approximations. However, they have little advantage for the Poisson and binomial distributions.

Conclusions

The proposed method is suitable for sample size calculations for comparisons of means of highly skewed outcome variables.

Electronic supplementary material

The online version of this article (doi:10.1186/s12874-015-0023-0) contains supplementary material, which is available to authorized users.