Molecular Transport and Reactivity in Confinement

For decades, tremendous efforts have been made through extensive experimental, theoretical and molecular simulated approaches to study numerous extraordinary phenomenon occur at sub-surface environments. As parts of such expedition, the works presented in this thesis employ (1) molecular dynamics (MD) simulations to investigate different structural and dynamic properties of confined fluids and (2) reactive ensemble Monte Carlo (RxMC) to explore thermodynamic properties of carbon dioxide methanation at nano-confinement. At the beginning, a series of studies by MD were conducted to examine the adsorption, structures and diffusion of (1) pure hydrocarbon and (2) mixtures of different hydrocarbons and carbon dioxide in silica pores at sub-, near-, and super-critical conditions. At equilibrium, pronounced layering was observed for propane near the pore surface. Counterintuitively, simulated MD results, in agreement with experimental quasielastic incoherent neutron scattering data, reveal that pure propane confined in silica meso-pore yields higher selfdiffusivity at higher loading, isothermally. In the case of binary mixture, CO2 preferential adsorption on the pore surface is likely to attenuate the surface adsorption of hydrocarbon, lower the activation energy for hydrocarbon diffusivity, and consequently enhance hydrocarbon mobility at low CO2 loading. At high CO2 loading, hydrocarbon diffusivity is hindered by molecular crowding. Hence, the non-monotonic change in hydrocarbon selfdiffusion coefficients as functions of CO2 concentration displays local maxima. On the other hand, results obtained from RxMC simulations show strong dependency of the confined reaction equilibrium conversions 2 and equilibrium constants Kp on the pore size, pore chemistry and pore morphology. Conditions that facilitate the preferential adsorption of water on the pore walls (e.g., small pore width, high hydrophobicity of pore substrate, and rough pore surface) yield high 2 and Kp, with the possibility of changing significantly the equilibrium composition of the reactive system with respect to bulk observations

Analysis of the Expression of Repetitive DNA Elements in Osteosarcoma

Osteosarcoma (OS) is a rare malignant bone tumor. It affects mostly young persons and has poor outcome with the present treatment. No improvement was observed since the introduction of chemotherapy. The better understanding of osteosarcoma development could indicate better management strategy. Repetitive DNA elements were found to play a role in cancer mechanism especially in epithelial tumors but not yet analyzed in osteosarcoma. We conducted the study to analyse the expression profile of repetitive elements (RE) in osteosarcoma. Methods: Fresh bone paired (tumor and normal bone) samples were obtained from excised parts of tumors of 18 patients with osteosarcoma. We performed sequencing of RNA extracted from 36 samples (18 tumor tissues and 18 normal bone for controls), mapped raw reads to the human genome and identified the REs. EdgeR package was used to analyse the difference in expression of REs between osteosarcoma and normal bone. Results: 82 REs were found differentially expressed (FDR < 0.05) between osteosarcoma and normal bone. Out of all significantly changed REs, 35 were upregulated and 47 were downregulated. HERVs (THE1C-int, LTR5, MER57F and MER87B) and satellite elements (HSATII, ALR-alpha) were the most significantly differential expressed elements between osteosarcoma and normal tissues. These results suggest significant impact of REs in the osteosarcoma. The role of REs should be further studied to understand the mechanism they have in the genesis of osteosarcoma

Red blood cell extracellular vesicles as robust carriers of RNA-based therapeutics

One of the major challenges of RNA-based therapeutics is the method for delivery of RNA molecules. In a recent article (Nat Commun 9(1):2359), we described a novel delivery platform for RNA-based drugs using red blood cell extracellular vesicles which can efficiently deliver both small and large RNAs to solid and liquid tumours. Our RBCEVs platform features exceptional merits over conventional RNA delivery methods in biosafety, biocompatibility, efficiency, accessibility, and cost effectiveness

Subgraph spotting in graph representations of comic book images

This is the author accepted manuscript. The final version is available from Elsevier via the DOI in this record Graph-based representations are the most powerful data structures for extracting, representing and preserving the structural information of underlying data. Subgraph spotting is an interesting research problem, especially for studying and investigating the structural information based content-based image retrieval (CBIR) and query by example (QBE) in image databases. In this paper we address the problem of lack of freely available ground-truthed datasets for subgraph spotting and present a new dataset for subgraph spotting in graph representations of comic book images (SSGCI) with its ground-truth and evaluation protocol. Experimental results of two state-of-the-art methods of subgraph spotting are presented on the new SSGCI dataset.University of La Rochelle (France

Crashworthiness analysis and optimization of standard and windowed multi-cell hexagonal tubes

This is an accepted manuscript of an article published by Springer in Structural and Multidisciplinary Optimization on 07/01/2021, available online: https://doi.org/10.1007/s00158-020-02794-y The accepted version of the publication may differ from the final published version.Recently, multi-cell structures have received increased attention for crashworthiness applications due to their superior energy absorption capability. However, such structures were featured with high peak collapsing force (PCL) forming a serious safety concern, and this limited their application for vehicle structures. Accordingly, this paper proposes windowed shaped cuttings as a mechanism to reduce the high PCL of the multi-cell hexagonal tubes and systemically investigates the axial crushing of different windowed multi-cell tubes and also seeks for their optimal crashworthiness design. Three different multi-cell configurations were constructed using wall-to-wall (WTW) and corner-to-corner (CTC) connection webs. Validated finite element models were generated using explicit finite element code, LS-DYNA, and were used to run crush simulations on the studied structures. The crashworthiness responses of the multi-cell standard tubes (STs), i.e., without windows, and multi-cell windowed tubes (WTs) were determined and compared. The WTW connection type was found to be more effective for STs and less favorable for WTs. Design of experiments (DoE), response surface methodology (RSM), and multiple objective particle swarm optimization (MOPSO) tools were employed to find the optimal designs of the different STs and WTs. Furthermore, parametric analysis was conducted to uncover the effects of key geometrical parameters on the main crashworthiness responses of all studied structures. The windowed cuttings were found to be able to slightly reduce the PCL of the multi-cell tubes, but this reduction was associated with a major negative implication on their energy absorption capability. This work provides useful insights on designing effective multi-cell structures suitable for vehicle crashworthiness applications.This research is funded by the Vietnam National Foundation for Science and Technology Development (NAFOSTED) under grant number 107.99-2019.02.Published onlin

DNA demethylases target promoter transposable elements to positively regulate stress responsive genes in Arabidopsis

© 2014 Le et al. Background: DNA demethylases regulate DNA methylation levels in eukaryotes. Arabidopsis encodes four DNA demethylases, DEMETER (DME), REPRESSOR OF SILENCING 1 (ROS1), DEMETER-LIKE 2 (DML2), and DML3. While DME is involved in maternal specific gene expression during seed development, the biological function of the remaining DNA demethylases remains unclear. Results: We show that ROS1, DML2, and DML3 play a role in fungal disease resistance in Arabidopsis. A triple DNA demethylase mutant, rdd (ros1 dml2 dml3), shows increased susceptibility to the fungal pathogen Fusarium oxysporum. We identify 348 genes differentially expressed in rdd relative to wild type, and a significant proportion of these genes are downregulated in rdd and have functions in stress response, suggesting that DNA demethylases maintain or positively regulate the expression of stress response genes required for F. oxysporum resistance. The rdd-downregulated stress response genes are enriched for short transposable element sequences in their promoters. Many of these transposable elements and their surrounding sequences show localized DNA methylation changes in rdd, and a general reduction in CHH methylation, suggesting that RNA-directed DNA methylation (RdDM), responsible for CHH methylation, may participate in DNA demethylase-mediated regulation of stress response genes. Many of the rdd-downregulated stress response genes are downregulated in the RdDM mutants nrpd1 and nrpe1, and the RdDM mutants nrpe1 and ago4 show enhanced susceptibility to F. oxysporum infection. Conclusions: Our results suggest that a primary function of DNA demethylases in plants is to regulate the expression of stress response genes by targeting promoter transposable element sequences

No time for change? Impact of contextual factors on the effect of training primary care healthcare workers in Kyrgyzstan and Vietnam on how to manage asthma in children - A FRESH AIR implementation study.

BACKGROUND: Training is a common and cost-effective way of trying to improve quality of care in low- and middle-income countries but studies of contextual factors for the successful translation of increased knowledge into clinical change are lacking, especially in primary care. The purpose of this study was to assess the impact of contextual factors on the effect of training rural healthcare workers in Kyrgyzstan and Vietnam on their knowledge and clinical performance in managing pediatric patients with respiratory symptoms. METHODS: Primary care health workers in Kyrgyzstan and Vietnam underwent a one-day training session on asthma in children under five. The effect of training was measured on knowledge and clinical performance using a validated questionnaire, and by direct clinical observations. RESULTS: Eighty-one healthcare workers participated in the training. Their knowledge increased by 1.1 Cohen's d (CI: 0.7 to 1.4) in Kyrgyzstan where baseline performance was lower and 1.5 Cohen's d (CI: 0.5 to 2.5) in Vietnam. Consultations were performed by different types of health care workers in Kyrgyzstan and there was a 79.1% (CI 73.9 to 84.3%) increase in consultations where at least one core symptom of respiratory illness was asked. Only medical doctors participated in Vietnam, where the increase was 25.0% (CI 15.1 to 34.9%). Clinical examination improved significantly after training in Kyrgyzstan. In Vietnam, the number of actions performed generally declined. The most pronounced difference in contextual factors was consultation time, which was median 15 min in Kyrgyzstan and 2 min in Vietnam. DISCUSSION AND CONCLUSION: The effects on knowledge of training primary care health workers in lower middle-income countries in diagnosis and management of asthma in children under five only translated into changes in clinical performance where consultation time allowed for changes to clinical practice, emphasizing the importance of considering contextual factors in order to succeed in behavioral change after training

miR-7 Controls the Dopaminergic/Oligodendroglial Fate through Wnt/\u3b2-catenin Signaling Regulation

During the development of the central nervous system, the proliferation of neural progenitors and differentiation of neurons and glia are tightly regulated by different transcription factors and signaling cascades, such as the Wnt and Shh pathways. This process takes place in cooperation with several microRNAs, some of which evolutionarily conserved in vertebrates, from teleosts to mammals. We focused our attention on miR-7, as its role in the regulation of cell signaling during neural development is still unclear. Specifically, we used human stem cell cultures and whole zebrafish embryos to study, in vitro and in vivo, the role of miR-7 in the development of dopaminergic (DA) neurons, a cell type primarily affected in Parkinson's disease. We demonstrated that the zebrafish homologue of miR-7 (miR-7a) is expressed in the forebrain during the development of DA neurons. Moreover, we identified 143 target genes downregulated by miR-7, including the neural fate markers TCF4 and TCF12, as well as the Wnt pathway effector TCF7L2. We then demonstrated that miR-7 negatively regulates the proliferation of DA-progenitors by inhibiting Wnt/\u3b2-catenin signaling in zebrafish embryos. In parallel, miR-7 positively regulates Shh signaling, thus controlling the balance between oligodendroglial and DA neuronal cell fates. In summary, this study identifies a new molecular cross-talk between Wnt and Shh signaling pathways during the development of DA-neurons. Being mediated by a microRNA, this mechanism represents a promising target in cell differentiation therapies for Parkinson's disease