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We consider a class of chance-constrained combinatorial optimization problems, which we refer to as probabilistic partial set-covering (PPSC) problems. Given a prespecified risk level $\epsilon\in[...

Learning directed acyclic graphs (DAGs) from data is a challenging task both in theory and in practice, because the number of possible DAGs scales superexponentially with the number of nodes. In this paper, we study the problem of learning an optimal DAG from continuous observational data. We cast this problem in the form of a mathematical programming model that can naturally incorporate a superstructure to reduce the set of possible candidate DAGs. We use a negative log-likelihood score function with both [Formula: see text] and [Formula: see text] penalties and propose a new mixed-integer quadratic program, referred to as a layered network (LN) formulation. The LN formulation is a compact model that enjoys as tight an optimal continuous relaxation value as the stronger but larger formulations under a mild condition. Computational results indicate that the proposed formulation outperforms existing mathematical formulations and scales better than available algorithms that can solve the same problem with only [Formula: see text] regularization. In particular, the LN formulation clearly outperforms existing methods in terms of computational time needed to find an optimal DAG in the presence of a sparse superstructure.

Liver transplantation is the only effective therapy for patients with decompensated cirrhosis and fulminant liver failure. However, due to a shortage of donor livers and complications associated with immune suppression, there is an urgent need for new therapeutic strategies for patients with end-stage liver diseases. Given their unique function in self-renewal and differentiation potential, stem cells might be used to regenerate damaged liver tissue. Recent studies have shown that stem cell-based therapies can improve liver function in a mouse model of hepatic failure. Moreover, acellular liver scaffolds seeded with hepatocytes produced functional bioengineered livers for organ transplantation in preclinical studies. The therapeutic potential of stem cells or their differentiated progenies will depend on their capacity to differentiate into mature and functional cell types after transplantation. It will also be important to devise methods to overcome their genomic instability, immune reactivity, and tumorigenic potential. We review directions and advances in the use of mesenchymal stem cells and their derived hepatocytes for liver regeneration. We also discuss the potential applications of hepatocytes derived from human pluripotent stem cells and challenges to using these cells in treating end-stage liver disease.

We consider a class of risk-averse submodular maximization problems (RASM) where the objective is the conditional value-at-risk (CVaR) of a random nondecreasing submodular function at a given risk level. We propose valid inequalities and an exact general method for solving RASM under the assumption that we have an efficient oracle that computes the CVaR of the random function. We demonstrate the proposed method on a stochastic set covering problem that admits an efficient CVaR oracle for the random coverage function.

Background Fulminant liver failure (FLF) is a life-threatening disease. Methods Lethal FLF was induced by ischemia-reperfusion (I-R) injury in mini-pigs, and MSCs were infused via splenic vein after reperfusion. Results Accumulated survival within 28 days was significantly improved by MSCs (P = 0.0348). Notably, MSCs maintained blood-gas homeostasis in the first 24 hours and prevented FLF-induced elevation of prothrombin time, international normalized ratio, and creatinine and ammonia levels in the first 3 days. With MSCs, serum levels of liver enzymes gradually decreased after 3 days, and platelet count was back to normal at 1 week of FLF. MSCs promoted liver regeneration within 2 weeks and differentiated into functional hepatocytes at 2-4 weeks after transplantation, evidenced by increase in Ki67-positive cells, detectable human hepatocyte growth factor, human vascular endothelial growth factor, human hepatocyte-specific antigen, and human albumin-expressing cells in the liver at different time points. Reactive oxidative species (ROS) were accumulated after FLF and eliminated at 4 weeks after MSC transplantation. Conclusions Together, MSCs prolong the survival and prevent lethal sequelae of I-R injury-induced FLF by maintenance of liver-function homeostasis and rescue of ROS in the acute stage and by homing and differentiation into hepatocytes in the subacute stage.

In vitro differentiation of stem cells into specific cell lineages provides a stable cell supply for cell therapy and tissue engineering. Therefore, understanding the mechanisms underlying such differentiation processes is critical for generating committed lineage-specific cell progenies effectively. We previously developed a two-step protocol to differentiate mesenchymal stromal cells (MSCs) into hepatocyte-like cells. Since hepatic differentiation involves mesenchymal-epithelial transition (MET), we hypothesize that promoting MET could further accelerate the differentiation process. Ras-related C3 botulinum toxin substrate 1 (Rac1) is involved in actin polymerization and its role in MET was investigated in the study. Our results showed that inhibition of Rac1 activation by Rac1-specific inhibitor, NSC23766, led to cells favoring epithelial morphology and being more packed during hepatic differentiation. In addition, Rac1 inhibition accelerated the upregulation of hepatic marker genes accompanied by more mature hepatic functions. Taken together, promotion of MET by inhibiting Rac1 accelerates the hepatic differentiation of MSCs. Our findings open a new prospect of directing the commitment of MSCs by manipulating cell morphology and cytoskeleton arrangement through small molecules. The results provide further insight into scaffold design for rapid production of MSC-differentiated hepatocytes.

Background We previously reported that mesenchymal stem cells (MSCs) possess therapeutic effects in a murine model of carbon tetrachloride-induced acute liver failure. In the study, we observed that the majority of repopulated hepatocytes were of recipient origin and were adjacent to transplanted MSCs; only a low percentage of repopulated hepatocytes were from transplanted MSCs. The findings indicate that MSCs guided the formation of new hepatocytes. Exosomes are important messengers for paracrine signaling delivery. The aim of this study is to investigate the paracrine effects, in particular, the effects of exosomes from MSCs, on hepatocytes. Methods Mature hepatocytes were isolated from murine liver by a two-step perfusion method with collagenase digestion. MSCs were obtained from murine bone marrow, and conditioned medium (CM) from MSC culture was then collected. Time-lapse imaging was used for observation of cell morphological change induced by CM on hepatocytes. In addition, expression of markers for hepatic progenitors including oval cells, intrahepatic stem cells, and hepatoblasts were analyzed. Results Treatment with the CM promoted the formation of small oval cells from hepatocytes; time-lapse imaging demonstrated the change from epithelial to oval cell morphology at the single hepatocyte level. Additionally, expression of EpCAM and OC2, markers of hepatic oval cells, was upregulated. Also, the number of EpCAMhigh cells was increased after CM treatment. The EpCAMhigh small oval cells possessed colony-formation ability; they also expressed cytokeratin 18 and were able to store glycogen upon induction of hepatic differentiation. Furthermore, exosomes from MSC-CM could induce the conversion of mature hepatocytes to EpCAMhigh small oval cells. Conclusions In summary, paracrine signaling through exosomes from MSCs induce the conversion of hepatocytes into hepatic oval cells, a mechanism of action which has not been reported regarding the therapeutic potentials of MSCs in liver regeneration. Exosomes from MSCs may therefore be used to treat liver diseases. Further studies are required for proof of concept of this approach. Electronic supplementary material The online version of this article (doi:10.1186/s13287-017-0560-z) contains supplementary material, which is available to authorized users.

There is a growing interest in cell therapies using mesenchymal stromal cells (MSCs) for repairing bone defects. MSCs have the ability to differentiate into osteoprogenitors and osteoblasts as well as to form calcified bone matrix. However, the molecular mechanisms governing mineralization during osteogenic differentiation remain unclear. Non-collagenous proteins in the extracellular matrix are believed to control different aspects of the mineralization. Since osteocalcin is the most abundant non-collagenous bone matrix protein, the purpose of this study is to investigate the roles of osteocalcin in mineral species production during osteogenesis of MSCs. Using Raman spectroscopy, we found that the maturation of mineral species was affected by osteocalcin expression level. After osteocalcin was knocked down, the mineral species maturation was delayed and total hydroxyapatite was lower than the control group. In addition, the expression of osteogenic marker genes, including RUNX2, alkaline phosphatase, type I collagen, and osteonectin, was downregulated during osteogenic differentiation compared to the control group; whereas gene expression of osterix was upregulated after the knockdown. Together, osteocalcin plays an essential role for the maturation of mineral species and modulates osteogenic differentiation of MSCs. The results offer new insights into the enhancement of new bone formation, such as for the treatments of osteoporosis and fracture healing.

Lineage commitment and differentiation of mesenchymal stromal cells (MSCs) into osteoblasts in vitro is enhanced by a potent synthetic form of glucocorticoid (GC), dexamethasone (Dex). Paradoxically, when used chronically in patients, GCs exert negative effects on bone, a phenomenon known as glucocorticoid-induced osteoporosis in clinical practice. The mechanism on how GC differentially affects bone precursor cells to become mature osteoblasts during osteogenesis remains elusive. In this study, the dose and temporal regulation of Dex on MSC differentiation into osteoblasts were investigated. We found that continuous Dex treatment led to a net reduction of the maturation potential of differentiating osteoblasts. This phenomenon correlated with a decrease in glucocorticoid receptor (GR) expression, hastened degradation, and impaired sub cellular localization. Similarly, Histone Deacetylase 6 (HDAC6) expression was found to be regulated by Dex, co-localized with GR and this GR-HDAC6 complex occupied the promoter region of the osteoblast late marker osteocalcin (OCN). Combinatorial inhibition of HDAC6 and GR enhanced OCN expression. Together, the cross-talk between the Dex effector molecule GR and the inhibitory molecule HDAC6 provided mechanistic explanation of the bimodal effect of Dex during osteogenic differentiation of MSCs. These findings may provide new directions of research to combat glucocorticoid-induced osteoporosis.

Mesenchymal stem cells (MSCs) have been shown to possess immunomodulatory properties. Systemic lupus erythematosus is an autoimmune disease that results in nephritis and subsequent destruction of renal microstructure. We investigated whether transplantation of human umbilical cord blood-derived MSCs (uMSCs) is useful in alleviating lupus nephritis in a murine model. It was found that uMSCs transplantation significantly delayed the development of proteinuria, decreased anti-dsDNA, alleviated renal injury, and prolonged the life span. There was a trend of decreasing T-helper (Th) 1 cytokines (IFN-γ, IL-2) and proinflammatory cytokines (TNF-α, IL-6, IL-12) and increasing Th2 cytokines (IL-4, IL-10). The in vitro coculture experiments showed that uMSCs only inhibited lymphocytes and splenocytes proliferation but not mesangial cells. Long-term engraftment of uMSCs in the kidney was not observed either. Together, these findings indicated that uMSCs were effective in decreasing renal inflammation and alleviating experimental lupus nephritis by inhibiting lymphocytes, inducing polarization of Th2 cytokines, and inhibition of proinflammatory cytokines production rather than direct engraftment and differentiating into renal tissue. Therapeutic effects demonstrated in this preclinical study support further exploration of the possibility to use uMSCs from mismatched donors in lupus nephritis treatment.

osteoblasts, adipocytes, chondrocytes, tenocytes, and myoblasts, and contribute to the regeneration of a variety of mesenchymal tissues. Adipose tissue represents a rich source of mesenchymal stem cells, and provides an abundant and accessible source of adult stem cells with minimal patient discomfort. Isolation of adipose tissue-derived stem cells (ADSCs) has primarily been achieved with Liberase HI, which is composed of Clostridium histolyticum collagenases I and II and thermolysin. All Liberase preparations contain endotoxin, which is harmful for cell viability. The recombinant production of Liberase enzymes is marred by the instability of collagenase I. The matrix metalloproteinases (MMPs) are a family of enzymes capable of catalyzing the degradation of virtually all ECM components, including collagens, laminin, fibronectin, and elastin. We have explored recombinant MMP cocktails for the efficient isolation of ADSCs, and found one approach (Matrizyme I) that (1) is effective in the isolation of stem cells from adipose tissue, (2) has similar isolation efficiencies as bacterial collagenase, and (3) is stored in an inactive form that can be activated when needed. The use of recombinant MMPs is very significant, because without the highest quality of connective tissue degrading enzymes it is virtually impossible to liberate viable ADSCs with good and stable proliferative capabilities.

Introduction Mesenchymal stromal cells (MSCs) are well known for their application potential in tissue engineering. We previously reported that MSCs are able to differentiate into hepatocytes in vitro. However, conventional methods for estimating the maturation of hepatic differentiation require relatively large amounts of cell samples. Raman spectroscopy (RS), a photonic tool for acquisition of cell spectra by inelastic scattering, has been recently used as a label-free single-cell detector for biological applications including phenotypic changes and differentiation of cells and diagnosis. In this study, RS is used to real-time monitor the maturation of hepatic differentiation in live MSCs. Methods The MSCs were cultured on the type I collagen pre-coating substrate and differentiated into hepatocytes in vitro using a two-step protocol. The Raman spectra at different time points are acquired in the range 400–3000 cm–1and analyzed by quantification methods and principle component analysis during hepatic differentiation from the MSCs. Results The intensity of the broad band in the range 2800–3000 cm–1 reflects the amount of glycogen within lipochrome in differentiated hepatocytes. A high correlation coefficient between the glycogen amount and hepatic maturation was exhibited. Moreover, principle component analysis of the Raman spectra from 400 to 3000 cm–1 indicated that MSC-derived hepatocytes were close to the primary hepatocytes and were distinct from the undifferentiated MSCs. Conclusions In summary, RS can serve as a rapid, non-invasive, real-time and label-free biosensor and reflects changes in live cell components during hepatic differentiation. The use of RS may thus facilitate the detection of hepatic differentiation and maturation in stem cells. Such an approach may substantially improve the feasibility as well as shorten the time required compared to the conventional molecular biology methods.