BackgroundHarmonization techniques make different gene expression profiles and their sets compatible and ready for comparisons. Here we present a new bioinformatic tool termed Shambhala for harmonization of multiple human gene expression datasets obtained using different experimental methods and platforms of microarray hybridization and RNA sequencing.ResultsUnlike previously published methods enabling good quality data harmonization for only two datasets, Shambhala allows conversion of multiple datasets into the universal form suitable for further comparisons. Shambhala harmonization is based on the calibration of gene expression profiles using the auxiliary standardization dataset. Each profile is transformed to make it similar to the output of microarray hybridization platform Affymetrix Human Gene. This platform was chosen because it has the biggest number of human gene expression profiles deposited in public databases. We evaluated Shambhala ability to retain biologically important features after harmonization. The same four biological samples taken in multiple replicates were profiled independently using three and four different experimental platforms, respectively, then Shambhala-harmonized and investigated by hierarchical clustering.ConclusionOur results showed that unlike other frequently used methods: quantile normalization and DESeq/DESeq2 normalization, Shambhala harmonization was the only method supporting sample-specific and platform-independent biologically meaningful clustering for the data obtained from multiple experimental platforms.Electronic supplementary materialThe online version of this article (10.1186/s12859-019-2641-8) contains supplementary material, which is available to authorized users.

ABSTRACT

This first open-label pilot study demonstrates the feasibility and short-term safety of local CD34(+) cell therapy for SSc ischaemic complications.

Bioceramics are used to treat bone defects but in general do not induce formation of new bone, which is essential for regeneration process. Many aspects related to bioceramics synthesis, properties and biological response that are still unknown and, there is a great need for further development. In the most recent research efforts were aimed on creation of materials from biological precursors of apatite formation in humans. One possible precursor is octacalcium phosphate (OCP), which is believed to not only exhibit osteoconductivity but possess osteoinductive quality, the ability to induce bone formation. Here we propose a relatively simple route for OCP ceramics preparation with a specifically designed microstructure. Comprehensive study for OCP ceramics including biodegradation, osteogenic properties in ortopic and heterotopic models and limited clinical trials were performed that demonstrated enhanced biological behavior. Our results provide a possible new concept for the clinical applications of OCP ceramics.

Biocompatible ceramic fillers are capable of sustaining bone formation in the proper environment. The major drawback of these scaffolding materials is the absence of osteoinductivity. To overcome this limitation, bioengineered scaffolds combine osteoconductive components (biomaterials) with osteogenic features such as cells and growth factors. The bone marrow mesenchymal stromal cells (BMMSCs) and the β-tricalcium phosphate (β-TCP) are well-known and characterized in this regard. The present study was conducted to compare the properties of novel octacalcium phosphate ceramic (OCP) granules with β-TCP (Cerasorb(®)), gingiva-derived mesenchymal stromal cells (GMSCs) properties with the BMMSCs and osteogenic and angiogenic properties of a bioengineered composite based on OCP granules and the GMSCs. This study demonstrates that GMSCs and BMMSСs have a similar osteogenic capacity. The usage of OCP ceramic granules in combination with BMMSCs/GMSCs significantly affects the osteo- and angiogenesis in bone grafts of ectopic models.