HMCLab: a framework for solving diverse geophysical inverse problems using the Hamiltonian Monte Carlo method

The use of the probabilistic approach to solve inverse problems is becoming more popular in the geophysical community, thanks to its ability to address nonlinear forward problems and to provide uncertainty quantification. However, such strategy is often tailored to specific applications and therefore there is a lack of a common platform for solving a range of different geophysical inverse problems and showing potential and pitfalls. We demonstrate a common framework to solve such inverse problems ranging from, e.g, earthquake source location to potential field data inversion and seismic tomography. Within this approach, we can provide probabilities related to certain properties or structures of the subsurface. Thanks to its ability to address high-dimensional problems, the Hamiltonian Monte Carlo (HMC) algorithm has emerged as the state-of-the-art tool for solving geophysical inverse problems within the probabilistic framework. HMC requires the computation of gradients, which can be obtained by adjoint methods, making the solution of tomographic problems ultimately feasible. These results can be obtained with "HMCLab", a tool for solving a range of different geophysical inverse problems using sampling methods, focusing in particular on the HMC algorithm. HMCLab consists of a set of samplers and a set of geophysical forward problems. For each problem its misfit function and gradient computation are provided and, in addition, a set of prior models can be combined to inject additional information into the inverse problem. This allows users to experiment with probabilistic inverse problems and also address real-world studies. We show how to solve a selected set of problems within this framework using variants of the HMC algorithm and analyze the results. HMCLab is provided as an open source package written both in Python and Julia, welcoming contributions from the community.Comment: 21 pages, 4 figure

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Proangiogenic Hypoxia-Mimicking Agents Attenuate Osteogenic Potential of Adipose Stem/Stromal Cells

BACKGROUND: Insufficient vascularization hampers bone tissue engineering strategies for reconstructing large bone defects. Delivery of prolyl-hydroxylase inhibitors (PHIs) is an interesting approach to upregulate vascular endothelial growth factor (VEGF) by mimicking hypoxic stabilization of hypoxia-inducible factor-1alpha (HIF-1α). This study assessed two PHIs: dimethyloxalylglycine (DMOG) and baicalein for their effects on human adipose tissue-derived mesenchymal stem/stromal cells (AT-MSCs). METHODS: Isolated AT-MSCs were characterized and treated with PHIs to assess the cellular proliferation response. Immunostaining and western-blots served to verify the HIF-1α stabilization response. The optimized concentrations for long-term treatment were tested for their effects on the cell cycle, apoptosis, cytokine secretion, and osteogenic differentiation of AT-MSCs. Gene expression levels were evaluated for alkaline phosphatase (ALPL), bone morphogenetic protein 2 (BMP2), runt-related transcription factor 2 (RUNX2), vascular endothelial growth factor A (VEGFA), secreted phosphoprotein 1 (SPP1), and collagen type I alpha 1 (COL1A1). In addition, stemness-related genes Kruppel-like factor 4 (KLF4), Nanog homeobox (NANOG), and octamer-binding transcription factor 4 (OCT4) were assessed. RESULTS: PHIs stabilized HIF-1α in a dose-dependent manner and showed evident dose- and time dependent antiproliferative effects. With doses maintaining proliferation, DMOG and baicalein diminished the effect of osteogenic induction on the expression of RUNX2, ALPL, and COL1A1, and suppressed the formation of mineralized matrix. Suppressed osteogenic response of AT-MSCs was accompanied by an upregulation of stemness-related genes. CONCLUSION: PHIs significantly reduced the osteogenic differentiation of AT-MSCs and rather upregulated stemness-related genes. PHIs proangiogenic potential should be weighed against their longterm direct inhibitory effects on the osteogenic differentiation of AT-MSCs.Peer reviewe

Monocyte-derived extracellular vesicles stimulate cytokinesecretion and gene expression of matrixmetalloproteinases by mesenchymal stem/stromal cells

Intercellular communication is essential in bone remodelling to ensure that new bone is formed with only temporary bone loss. Monocytes (MCs) and osteoclasts actively take part in controlling bone remodelling by providing signals that promote osteogenic differentiation of mesenchymal stem/stromal cells (MSCs). Extracellular vesicles (EVs) have attracted attention as regulators of bone remodelling. EVs facilitate intercellular communication by transferring a complex cargo of biologically active molecules to target cells. In the present study, we evaluated the potency of EVs from MCs and osteoclasts to induce a lineage-specific response in MSCs. We analysed gene expression and protein secretion by both adipose tissue-derived MSCs and bone marrow-derived MSCs after stimulation with EVs from lipopolysaccharide-activated primary human MCs and (mineral-resorbing) osteoclasts. Isolated EVs were enriched in exosomes (EVs of endosomal origin) and were free of cell debris. MC- and osteoclast-derived EVs were taken up by adipose tissue-derived MSCs. EVs from activated MCs promoted the secretion of cytokines by MSCs, which may represent an immunomodulatory mechanism. MC-derived EVs also upregulated the expression of genes encoding for matrix metalloproteinases. Therefore, we hypothesize that MCs facilitate tissue remodelling through EV-mediated signalling. We did not observe a significant effect of osteoclast-derived EVs on gene expression or protein secretion in MSCs. EV-mediated signalling might represent an additional mode of cell-cell signalling during the transition from injury and inflammation to bone regeneration and play an important role in the coupling between bone resorption and bone formation. DatabaseGene expression data are available in the GEO database under the accession number .Peer reviewe

Growth Response and Differentiation of Bone Marrow-Derived Mesenchymal Stem/Stromal Cells in the Presence of Novel Multiple Myeloma Drug Melflufen

Mesenchymal stem/stromal cells (MSCs) are self-renewing and multipotent progenitors, which constitute the main cellular compartment of the bone marrow stroma. Because MSCs have an important role in the pathogenesis of multiple myeloma, it is essential to know if novel drugs target MSCs. Melflufen is a novel anticancer peptide–drug conjugate compound for patients with relapsed refractory multiple myeloma. Here, we studied the cytotoxicity of melflufen, melphalan and doxorubicin in healthy human bone marrow-derived MSCs (BMSCs) and how these drugs affect BMSC proliferation. We established co-cultures of BMSCs with MM.1S myeloma cells to see if BMSCs increase or decrease the cytotoxicity of melflufen, melphalan, bortezomib and doxorubicin. We evaluated how the drugs affect BMSC differentiation into adipocytes and osteoblasts and the BMSC-supported formation of vascular networks. Our results showed that BMSCs were more sensitive to melflufen than to melphalan. The cytotoxicity of melflufen in myeloma cells was not affected by the co-culture with BMSCs, as was the case for melphalan, bortezomib and doxorubicin. Adipogenesis, osteogenesis and BMSC-mediated angiogenesis were all affected by melflufen. Melphalan and doxorubicin affected BMSC differentiation in similar ways. The effects on adipogenesis and osteogenesis were not solely because of effects on proliferation, seen from the differential expression of differentiation markers normalized by cell number. Overall, our results indicate that melflufen has a significant impact on BMSCs, which could possibly affect therapy outcome

Growth Response and Differentiation of Bone Marrow-Derived Mesenchymal Stem/Stromal Cells in the Presence of Novel Multiple Myeloma Drug Melflufen

Mesenchymal stem/stromal cells (MSCs) are self-renewing and multipotent progenitors, which constitute the main cellular compartment of the bone marrow stroma. Because MSCs have an important role in the pathogenesis of multiple myeloma, it is essential to know if novel drugs target MSCs. Melflufen is a novel anticancer peptide-drug conjugate compound for patients with relapsed refractory multiple myeloma. Here, we studied the cytotoxicity of melflufen, melphalan and doxorubicin in healthy human bone marrow-derived MSCs (BMSCs) and how these drugs affect BMSC proliferation. We established co-cultures of BMSCs with MM.1S myeloma cells to see if BMSCs increase or decrease the cytotoxicity of melflufen, melphalan, bortezomib and doxorubicin. We evaluated how the drugs affect BMSC differentiation into adipocytes and osteoblasts and the BMSC-supported formation of vascular networks. Our results showed that BMSCs were more sensitive to melflufen than to melphalan. The cytotoxicity of melflufen in myeloma cells was not affected by the co-culture with BMSCs, as was the case for melphalan, bortezomib and doxorubicin. Adipogenesis, osteogenesis and BMSC-mediated angiogenesis were all affected by melflufen. Melphalan and doxorubicin affected BMSC differentiation in similar ways. The effects on adipogenesis and osteogenesis were not solely because of effects on proliferation, seen from the differential expression of differentiation markers normalized by cell number. Overall, our results indicate that melflufen has a significant impact on BMSCs, which could possibly affect therapy outcome.Peer reviewe

Growth Response and Differentiation of Bone Marrow-Derived Mesenchymal Stem/Stromal Cells in the Presence of Novel Multiple Myeloma Drug Melflufen

Mesenchymal stem/stromal cells (MSCs) are self-renewing and multipotent progenitors, which constitute the main cellular compartment of the bone marrow stroma. Because MSCs have an important role in the pathogenesis of multiple myeloma, it is essential to know if novel drugs target MSCs. Melflufen is a novel anticancer peptide–drug conjugate compound for patients with relapsed refractory multiple myeloma. Here, we studied the cytotoxicity of melflufen, melphalan and doxorubicin in healthy human bone marrow-derived MSCs (BMSCs) and how these drugs affect BMSC proliferation. We established co-cultures of BMSCs with MM.1S myeloma cells to see if BMSCs increase or decrease the cytotoxicity of melflufen, melphalan, bortezomib and doxorubicin. We evaluated how the drugs affect BMSC differentiation into adipocytes and osteoblasts and the BMSC-supported formation of vascular networks. Our results showed that BMSCs were more sensitive to melflufen than to melphalan. The cytotoxicity of melflufen in myeloma cells was not affected by the co-culture with BMSCs, as was the case for melphalan, bortezomib and doxorubicin. Adipogenesis, osteogenesis and BMSC-mediated angiogenesis were all affected by melflufen. Melphalan and doxorubicin affected BMSC differentiation in similar ways. The effects on adipogenesis and osteogenesis were not solely because of effects on proliferation, seen from the differential expression of differentiation markers normalized by cell number. Overall, our results indicate that melflufen has a significant impact on BMSCs, which could possibly affect therapy outcome

Subglacial volcano monitoring with fibre-optic sensing: Grímsvötn, Iceland

We present a distributed acoustic sensing (DAS) experiment at Grímsvötn, Iceland. This is intended to investigate volcano-microseismicity at Grímsvötn specifically, and to assess the suitability of DAS as a subglacial volcano monitoring tool in general. In spring 2021, we trenched a 12 km long fiber-optic cable into the ice sheet around and within the caldera, followed by nearly one month of continuous recording. An image processing algorithm that exploits spatial coherence in DAS data detects on average ~100 events per day, almost 2 orders of magnitude more than in the regional earthquake catalog. A nonlinear Bayesian inversion reveals the presence of pronounced seismicity clusters, containing events with magnitudes between −3.4 and 1.7. Their close proximity to surface volcanic features suggests a geothermal origin. In addition to painting a fine-scale picture of seismic activity at Grímsvötn, this work confirms the potential of DAS in subglacial volcano monitoring

Chitosan/collagen/Mg, Se, Sr, Zn-substituted calcium phosphate scaffolds for bone tissue engineering applications : A growth factor free approach

According to the biomimetic bone scaffold design paradigm, a scaffold resembling natural bone tissue with molecular, structural and biological compatibility is needed to allow effective regeneration of bone tissue. Continuing our previous studies regarding scaffolds with chitosan matrix containing Mg, Se, Sr, Zn-substituted calcium phosphates (CaPs), the focus of this work was to further improve the properties of these growth factor-free scaffolds. By addition of collagen into the chitosan matrix at weight ratios of 100:0, 75:25, 50:50, 25:75 and 0:100, we aimed to better resemble natural bone tissue. Highly porous composite scaffolds based on chitosan and collagen, with 30 wt% of Mg, Se, Sr, Zn-substituted CaPs, were prepared by the freeze-gelation method. The scaffolds show a highly porous structure, with interconnected pores in the range of 20–350 μm and homogeneously dispersed CaPs. The added collagen further enhanced the stability measured during 28 days in simulated biological conditions. Live/dead and CyQUANT assays confirmed good viability and proliferation of human bone marrow-derived mesenchymal stem/stromal cells, while successful osteogenic differentiation was confirmed by alkaline phosphatase quantification and type I collagen immunocytochemical staining. Results indicated that the addition of collagen into the chitosan matrix containing Mg, Se, Sr, Zn-substituted CaPs improved the physicochemical and biological properties of the scaffolds.publishedVersionPeer reviewe