How to Simulate Quantum Measurement without Computing Marginals.

We describe and analyze algorithms for classically simulating measurement of an n-qubit quantum state in the standard basis, that is, sampling a bit string from the probability distribution determined by the Born rule. Our algorithms reduce the sampling task to computing poly(n) amplitudes of n-qubit states; unlike previously known techniques they do not require computation of marginal probabilities. Two classes of quantum states are considered: output states of polynomial-size quantum circuits, and ground states of local Hamiltonians with an inverse polynomial spectral gap. We show that our algorithms can significantly accelerate quantum circuit simulations based on tensor network contraction or low-rank stabilizer decompositions. As another striking consequence we obtain the first efficient classical simulation algorithm for measurement-based quantum computation with the surface code resource state on any planar graph and any schedule of measurements.

Improved Approximation Algorithms for Bounded-Degree Local Hamiltonians.

The low-temperature properties of interacting quantum systems are believed to require exponential resources to compute in the general case. Quantifying the extent to which such properties can be approximated using efficient algorithms remains a significant open challenge. Here, we consider the task of approximating the ground state energy of two-local quantum Hamiltonians with bounded-degree interaction graphs. Most existing algorithms optimize the energy over the set of product states. We propose and analyze a family of shallow quantum circuits that can be used to improve the approximation ratio achieved by a given product state. The algorithm takes as input an n-qubit product state with variance Var and improves its energy by an amount proportional to Var^{2}/n. In a typical case, this results in an extensive improvement in the estimated energy. We extend our results to k-local Hamiltonians and entangled initial states.

LentiRILES, a miRNA-ON sensor system for monitoring the functionality of miRNA in cancer biology and therapy.

A major unresolved challenge in miRNA biology is the capacity to monitor the spatiotemporal activity of miRNAs expressed in animal disease models. We recently reported that the miRNA-ON monitoring system called RILES (RNAi-inducible expression Luciferase system) implanted in lentivirus expression system (LentiRILES) offers unique opportunity to decipher the kinetics of miRNA activity in vitro, in relation with their intracellular trafficking in glioblastoma cells. In this study, we describe in detail the method for the production of LentiRILES stable cell lines and employed it in several applications in the field of miRNA biology and therapy. We show that LentiRILES is a robust, highly specific and sensitive miRNA sensor system that can be used in vitro as a single-cell miRNA monitoring method, cell-based screening platform for miRNA therapeutics and as a tool to analyse the structure-function relationship of the miRNA duplex. Furthermore, we report the kinetics of miRNA activity upon the intracranial delivery of miRNA mimics in an orthotopic animal model of glioblastoma. This information is exploited to evaluate the tumour suppressive function of miRNA-200c as locoregional therapeutic modality to treat glioblastoma. Our data provide evidence that LentiRILES is a robust system, well suited to resolve the activity of endogenous and exogenously expressed miRNAs from basic research to gene and cell therapy.

LIMK2-1, a new isoform of human LIMK2, regulates actin cytoskeleton remodeling via a different signaling pathway than that of its two homologs, LIMK2a and LIMK2b.

LIMK1 and LIMK2 (LIMKs, LIM kinases) are kinases that play a crucial role in cytoskeleton dynamics by independently regulating both actin filament and microtubule remodeling. LIMK1 and, more recently, LIMK2 have been shown to be involved in cancer development and metastasis, resistance of cancer cells to microtubule-targeted treatments, neurological diseases, and viral infection. LIMKs have thus recently emerged as new therapeutic targets. Databanks describe three isoforms of human LIMK2: LIMK2a, LIMK2b, and LIMK2-1. Evidence suggests that they may not have completely overlapping functions. We biochemically characterized the three isoforms to better delineate their potential roles, focusing on LIMK2-1, which has only been described at the mRNA level in a single study. LIMK2-1 has a protein phosphatase 1 (PP1) inhibitory domain at its C-terminus which its two counterparts do not. We showed that the LIMK2-1 protein is indeed synthesized. LIMK2-1 does not phosphorylate cofilin, the canonical substrate of LIMKs, although it has kinase activity and promotes actin stress fiber formation. Instead, it interacts with PP1 and partially inhibits its activity towards cofilin. Our data suggest that LIMK2-1 regulates actin cytoskeleton dynamics by preventing PP1-mediated cofilin dephosphorylation, rather than by directly phosphorylating cofilin as its two counterparts, LIMK2a and LIMK2b. This specificity may allow for tight regulation of the phospho-cofilin pool, determining the fate of the cell.

Polynomial-Time Classical Simulation of Quantum Ferromagnets.

We consider a family of quantum spin systems which includes, as special cases, the ferromagnetic XY model and ferromagnetic Ising model on any graph, with or without a transverse magnetic field. We prove that the partition function of any model in this family can be efficiently approximated to a given relative error ε using a classical randomized algorithm with runtime polynomial in ε^{-1}, system size, and inverse temperature. As a consequence, we obtain a polynomial time algorithm which approximates the free energy or ground energy to a given additive error. We first show how to approximate the partition function by the perfect matching sum of a finite graph with positive edge weights. Although the perfect matching sum is not known to be efficiently approximable in general, the graphs obtained by our method have a special structure which facilitates efficient approximation via a randomized algorithm due to Jerrum and Sinclair.

Correlation Length versus Gap in Frustration-Free Systems.

Hastings established exponential decay of correlations for ground states of gapped quantum many-body systems. A ground state of a (geometrically) local Hamiltonian with spectral gap ε has correlation length ξ upper bounded as ξ=O(1/ε). In general this bound cannot be improved. Here we study the scaling of the correlation length as a function of the spectral gap in frustration-free local Hamiltonians, and we prove a tight bound ξ=O(1/sqrt[ε]) in this setting. This highlights a fundamental difference between frustration-free and frustrated systems near criticality. The result is obtained using an improved version of the combinatorial proof of correlation decay due to Aharonov, Arad, Vazirani, and Landau.

Improved Classical Simulation of Quantum Circuits Dominated by Clifford Gates.

We present a new algorithm for classical simulation of quantum circuits over the Clifford+T gate set. The runtime of the algorithm is polynomial in the number of qubits and the number of Clifford gates in the circuit but exponential in the number of T gates. The exponential scaling is sufficiently mild that the algorithm can be used in practice to simulate medium-sized quantum circuits dominated by Clifford gates. The first demonstrations of fault-tolerant quantum circuits based on 2D topological codes are likely to be dominated by Clifford gates due to a high implementation cost associated with logical T gates. Thus our algorithm may serve as a verification tool for near-term quantum computers which cannot in practice be simulated by other means. To demonstrate the power of the new method, we performed a classical simulation of a hidden shift quantum algorithm with 40 qubits, a few hundred Clifford gates, and nearly 50 T gates.

Enhanced lipid and biomass production by a newly isolated and identified marine microalga.

BACKGROUND: The increasing demand for microalgae lipids as an alternative to fish has encouraged researchers to explore oleaginous microalgae for food uses. In this context, optimization of growth and lipid production by the marine oleaginous V2-strain-microalgae is of great interest as it contains large amounts of mono-unsaturated (MUFAs) and poly-unsaturated fatty acids (PUFAs). METHODS: In this study, the isolated V2 strain was identified based on 23S rRNA gene. Growth and lipid production conditions were optimized by using the response surface methodology in order to maximize its cell growth and lipid content that was quantified by both flow cytometry and the gravimetric method. The intracellular lipid bodies were detected after staining with Nile red by epifluorescence microscopy. The fatty acid profile of optimal culture conditions was determined by gas chromatography coupled to a flame ionization detector. RESULTS: The phenotypic and phylogenetic analyses showed that the strain V2 was affiliated to Tetraselmis genus. The marine microalga is known as an interesting oleaginous species according to its high lipid production and its fatty acid composition. The optimization process showed that maximum cell abundance was achieved under the following conditions: pH: 7, salinity: 30 and photosynthetic light intensity (PAR): 133 µmol photons.m-2.s-1. In addition, the highest lipid content (49 ± 2.1% dry weight) was obtained at pH: 7, salinity: 37.23 and photosynthetic light intensity (PAR): 188 µmol photons.m-2.s-1. The fatty acid profile revealed the presence of 39.2% and 16.1% of total fatty acids of mono-unsaturated fatty acids (MUFAs) and poly-unsaturated fatty acids (PUFAs), respectively. Omega 3 (ω3), omega 6 (ω6) and omega 9 (ω9) represented 5.28%, 8.12% and 32.8% of total fatty acids, respectively. CONCLUSIONS: This study showed the successful optimization of salinity, light intensity and pH for highest growth, lipid production and a good fatty acid composition, making strain V2 highly suitable for food and nutraceutical applications.

Universal adiabatic quantum computation via the space-time circuit-to-Hamiltonian construction.

We show how to perform universal adiabatic quantum computation using a Hamiltonian which describes a set of particles with local interactions on a two-dimensional grid. A single parameter in the Hamiltonian is adiabatically changed as a function of time to simulate the quantum circuit. We bound the eigenvalue gap above the unique ground state by mapping our model onto the ferromagnetic XXZ chain with kink boundary conditions; the gap of this spin chain was computed exactly by Koma and Nachtergaele using its q-deformed version of SU(2) symmetry. We also discuss a related time-independent Hamiltonian which was shown by Janzing to be capable of universal computation. We observe that in the limit of large system size, the time evolution is equivalent to the exactly solvable quantum walk on Young's lattice.

Exogenous mRNA delivery and bioavailability in gene transfer mediated by piggyBac transposition.

BACKGROUND: Up to now, the different uptake pathways and the subsequent intracellular trafficking of plasmid DNA have been largely explored. By contrast, the mode of internalization and the intracellular routing of an exogenous mRNA in transfected cells are poorly investigated and remain to be elucidated. The bioavailability of internalized mRNA depends on its intracellular routing and its potential accumulation in dynamic sorting sites for storage: stress granules and processing bodies. This question is of particular significance when a secure transposon-based system able to integrate a therapeutic transgene into the genome is used. Transposon vectors usually require two components: a plasmid DNA, carrying the gene of interest, and a source of transposase allowing the integration of the transgene. The principal drawback is the lasting presence of the transposase, which could remobilize the transgene once it has been inserted. Our study focused on the pharmacokinetics of the transposition process mediated by the piggyBac transposase mRNA transfection. Exogenous mRNA internalization and trafficking were investigated towards a better apprehension and fine control of the piggyBac transposase bioavailability. RESULTS: The mRNA prototype designed in this study provides a very narrow expression window of transposase, which allows high efficiency transposition with no cytotoxicity. Our data reveal that exogenous transposase mRNA enters cells by clathrin and caveolae-mediated endocytosis, before finishing in late endosomes 3 h after transfection. At this point, the mRNA is dissociated from its carrier and localized in stress granules, but not in cytoplasmic processing bodies. Some weaker signals have been observed in stress granules at 18 h and 48 h without causing prolonged production of the transposase. So, we designed an mRNA that is efficiently translated with a peak of transposase production 18 h post-transfection without additional release of the molecule. This confines the integration of the transgene in a very small time window. CONCLUSION: Our results shed light on processes of exogenous mRNA trafficking, which are crucial to estimate the mRNA bioavailability, and increase the biosafety of transgene integration mediated by transposition. This approach provides a new way for limiting the transgene copy in the genome and their remobilization by mRNA engineering and trafficking.

An E3-14.7K peptide that promotes microtubules-mediated transport of plasmid DNA increases polyplexes transfection efficiency.

Chemical vectors as cationic polymers and cationic lipids are promising alternatives to viral vectors for gene therapy. Beside endosome escape and nuclear import, plasmid DNA (pDNA) migration in the cytosol toward the nuclear envelope is also regarded as a limiting step for efficient DNA transfection with non-viral vectors. Here, the interaction between E3-14.7K and FIP-1 to favor migration of pDNA along microtubules is exploited. E3-14.7K is an early protein of human adenoviruses that interacts via FIP-1 (Fourteen.7K Interacting Protein 1) protein with the light-chain components of the human microtubule motor protein dynein (TCTEL1). This peptide is conjugated with pDNA and mediates interaction of pDNA in vitro with isolated microtubules as well as with microtubules in cellulo. Videomicroscopy and tracking treatment of images clearly demonstrate that P79-98/pDNA conjugate exhibits a linear transport with large amplitude along microtubules upon 2 h transfection with polyplexes whereas control pDNA conjugate exhibits small non-directional movements in the cytoplasm. Remarkably, P79-98/peGFP polyplexes enhance by a factor 2.5 (up to 76%) the number of transfected cells. The results demonstrate, for the first time, that the transfection efficiency of polyplexes can be drastically increased when the microtubules migration of pDNA is facilitated by a peptide allowing pDNA docking to TCTEL1. This is a real breakthrough in the non viral gene delivery field that opens hope to build artificial viruses.

Improvement of Antioxidant Defences in Keratinocytes Grown in Physioxia: Comparison of 2D and 3D Models.

Keratinocytes prevent skin photoaging by ensuring the defence against oxidative stress, an excessive production of reactive oxygen species (ROS). They are localized within the epidermis where the oxygen level (1-3% O2), named physioxia, is low compared to other organs. Oxygen is essential for life but also generates ROS. Most of the in vitro studies on keratinocyte antioxidant capacities are performed under atmospheric oxygen, named normoxia, which is very far from the physiological microenvironment, thus submitting cells to an overoxygenation. The present study is aimed at investigating the antioxidant status of keratinocyte grown under physioxia in both 2D and 3D models. First, we show that the basal antioxidant profiles of keratinocytes display important differences when comparing the HaCaT cell line, primary keratinocytes (NHEK), reconstructed epidermis (RHE), and skin explants. Physioxia was shown to promote a strong proliferation of keratinocytes in monolayers and in RHE, resulting in a thinner epidermis likely due to a slowdown in cell differentiation. Interestingly, cells in physioxia exhibited a lower ROS production upon stress, suggesting a better protection against oxidative stress. To understand this effect, we studied the antioxidant enzymes and reported a lower or equivalent level of mRNA for all enzymes in physioxia conditions compared to normoxia, but a higher activity for catalase and superoxide dismutases, whatever the culture model. The unchanged catalase amount, in NHEK and RHE, suggests an overactivation of the enzyme in physioxia, whereas the higher amount of SOD2 can explain the strong activity. Taken together, our results demonstrate the role of oxygen in the regulation of the antioxidant defences in keratinocytes, topic of particular importance for studying skin aging. Additionally, the present work points out the interest of the choice of both the keratinocyte culture model and the oxygen level to be as close as possible to the in situ skin.

Intrahippocampal Inoculation of Aß1-42 Peptide in Rat as a Model of Alzheimer's Disease Identified MicroRNA-146a-5p as Blood Marker with Anti-Inflammatory Function in Astrocyte Cells.

Circulating microRNAs (miRNAs) have aroused a lot of interest as reliable blood diagnostic biomarkers of Alzheimer's disease (AD). Here, we investigated the panel of expressed blood miRNAs in response to aggregated Aß1-42 peptides infused in the hippocampus of adult rats to mimic events of the early onset of non-familial AD disorder. Aß1-42 peptides in the hippocampus led to cognitive impairments associated with an astrogliosis and downregulation of circulating miRNA-146a-5p, -29a-3p, -29c-3p, -125b-5p, and-191-5p. We established the kinetics of expression of selected miRNAs and found differences with those detected in the APPswe/PS1dE9 transgenic mouse model. Of note, miRNA-146a-5p was exclusively dysregulated in the Aß-induced AD model. The treatment of primary astrocytes with Aß1-42 peptides led to miRNA-146a-5p upregulation though the activation of the NF-κB signaling pathway, which in turn downregulated IRAK-1 but not TRAF-6 expression. As a consequence, no induction of IL-1ß, IL-6, or TNF-α was detected. Astrocytes treated with a miRNA-146-5p inhibitor rescued IRAK-1 and changed TRAF-6 steady-state levels that correlated with the induction of IL-6, IL-1ß, and CXCL1 production, indicating that miRNA-146a-5p operates anti-inflammatory functions through a NF-κB pathway negative feedback loop. Overall, we report a panel of circulating miRNAs that correlated with Aß1-42 peptides' presence in the hippocampus and provide mechanistic insights into miRNA-146a-5p biological function in the development of the early stage of sporadic AD.

Lung inflammation and interstitial fibrosis by targeted alveolar epithelial type I cell death.

Introduction: The pathogenesis of chronic lung diseases is multifaceted with a major role of recurrent micro-injuries of the epithelium. While several reports clearly indicated a prominent role for surfactant-producing alveolar epithelial type 2 (AT2) cells, the contribution of gas exchange-permissive alveolar epithelial type 1 (AT1) cells has not been addressed yet. Here, we investigated whether repeated injury of AT1 cells leads to inflammation and interstitial fibrosis. Methods: We chose an inducible model of AT1 cell depletion following local diphtheria toxin (DT) administration using an iDTR flox/flox (idTRfl/fl) X Aquaporin 5CRE (Aqp5CRE) transgenic mouse strain. Results: We investigated repeated doses and intervals of DT to induce cell death of AT1 cells causing inflammation and interstitial fibrosis. We found that repeated DT administrations at 1ng in iDTRfl/fl X Aqp5CRE mice cause AT1 cell death leading to inflammation, increased tissue repair markers and interstitial pulmonary fibrosis. Discussion: Together, we demonstrate that depletion of AT1 cells using repeated injury represents a novel approach to investigate chronic lung inflammatory diseases and to identify new therapeutic targets.

ROS implication in a new antitumor strategy based on non-thermal plasma.

Non-thermal plasma (NTP) is generated by ionizing neutral gas molecules/atoms leading to a highly reactive gas at ambient temperature containing excited molecules, reactive species and generating transient electric fields. Given its potential to interact with tissue or cells without a significant temperature increase, NTP appears as a promising approach for the treatment of various diseases including cancer. The aim of our study was to evaluate the interest of NTP both in vitro and in vivo. To this end, we evaluated the antitumor activity of NTP in vitro on two human cancer cell lines (glioblastoma U87MG and colorectal carcinoma HCT-116). Our data showed that NTP generated a large amount of reactive oxygen species (ROS), leading to the formation of DNA damages. This resulted in a multiphase cell cycle arrest and a subsequent apoptosis induction. In addition, in vivo experiments on U87MG bearing mice showed that NTP induced a reduction of bioluminescence and tumor volume as compared to nontreated mice. An induction of apoptosis was also observed together with an accumulation of cells in S phase of the cell cycle suggesting an arrest of tumor proliferation. In conclusion, we demonstrated here that the potential of NTP to generate ROS renders this strategy particularly promising in the context of tumor treatment.

Expression of the Human Serotonin 5-HT7 Receptor Rescues Phenotype Profile and Restores Dysregulated Biomarkers in a Drosophila melanogaster Glioma Model.

Gliomas are the most common primary brain tumors in adults. Significant progress has been made in recent years in identifying the molecular alterations involved in gliomas. Among them, an amplification/overexpression of the EGFR (Epidermal Growth Factor Receptor) proto-oncogene and its associated signaling pathways have been widely described. However, current treatments remain ineffective for glioblastomas, the most severe forms. Thus, the identification of other pharmacological targets could open new therapeutic avenues. We used a glioma model in Drosophila melanogaster that results from the overexpression of constitutively active forms of EGFR and PI3K specifically in glial cells. We observed hyperproliferation of glial cells that leads to an increase in brain size and lethality at the third instar larval stage. After expression of the human serotonin 5-HT7 receptor in this glioma model, we observed a decrease in larval lethality associated with the presence of surviving adults and a return to a normal morphology of brain for some Drosophila. Those phenotypic changes are accompanied by the normalization of certain metabolic biomarkers measured by High-Resolution Magic Angle Spinning NMR (HR-MAS NMR). The 5-HT7R expression in glioma also restores some epigenetic modifications and characteristic markers of the signaling pathways associated with tumor growth. This study demonstrates the role of the serotonin 5-HT7 receptor as a tumor suppressor gene which is in agreement with transcriptomic analysis obtained on human glioblastomas.

T Lymphocyte Serotonin 5-HT7 Receptor Is Dysregulated in Natalizumab-Treated Multiple Sclerosis Patients.

Serotonin (5-HT) is known as a potent immune cell modulator in autoimmune diseases and should be protective in the pathogenesis of multiple sclerosis (MS). Nevertheless, there is limited knowledge about receptors involved in 5-HT effects as well as induced mechanisms. Among 5-HT receptors, the 5-HT7 receptor is able to activate naïve T cells and influence the inflammatory response; however, its involvement in the disease has never been studied so far. In this study, we collected blood sample from three groups: acute relapsing MS patients (ARMS), natalizumab-treated MS patients (NTZ), and control subjects. We investigated the 5-HT7 expression on circulating lymphocytes and evaluated the effects of its activation on cytokine production with peripheral blood mononuclear cell (PBMC) cultures. We found a significant increase in the 5-HT7 surface expression on T lymphocytes and on the different CD4+ T cell subsets exclusively in NTZ-treated patients. We also showed that the selective agonist 5-carboxamidotryptamine (5-CT)-induced 5-HT7R activation significantly promotes the production of IL-10, a potent immunosuppressive cytokine in PBMCs. This study provides for the first time a dysregulation of 5-HT7 expression in NTZ-MS patients and its ability to promote IL-10 release, suggesting its protective role. These findings strengthen the evidence that 5-HT7 may play a role in the immuno-protective mechanisms of NTZ in MS disease and could be considered as an interesting therapeutic target in MS.

Quantum state restoration and single-copy tomography for ground states of Hamiltonians.

Given a single copy of an unknown quantum state, the no-cloning theorem limits the amount of information that can be extracted from it. Given a gapped Hamiltonian, in most situations it is impractical to compute properties of its ground state, even though in principle all the information about the ground state is encoded in the Hamiltonian. We show in this Letter that if you know the Hamiltonian of a system and have a single copy of its ground state, you can use a quantum computer to efficiently compute its local properties. Specifically, in this scenario, we give efficient algorithms that copy small subsystems of the state and estimate the full statistics of any local measurement.

Selective human endothelial cell activation by chemokines as a guide to cell homing.

An original model of organo-specific, immortalized and stabilized endothelial cell lines was used to delineate the part played by some chemokines (CCL21, CX3CL1, CCL5 and CXCL12) and their receptors in endothelium organo-specificity. Chemokine receptor expression and chemokine presentation were investigated on organo-specific human endothelial cell lines. Although the chemokines showed distinct binding patterns for the various endothelial cell lines, these were not correlated with the expression of the corresponding receptors (CX3CR1, CXCR4, CCR5 and CCR7). Experiments with CCL21 on peripheral lymph node endothelial cells demonstrated that the chemokine did not co-localize with its receptor but was associated with extracellular matrix components. The specific activity of chemokines was clearly shown to be related to the endothelial cell origin. Indeed, CX3CL1 and CCL21 promoted lymphocyte recruitment by endothelial cells from the appendix and peripheral lymph nodes, respectively, while CX3CL1 pro-angiogenic activity was restricted to endothelial cells from the appendix and skin. The high specificity of the chemokine/endothelium interaction allowed the design of a direct in vitro endothelial cell targeting assay. This unique cellular model demonstrated a fundamental role for chemokines in conferring on the endothelium its organo-specificity and its potential for tissue targeting through the selective binding, presentation and activation properties of chemokines.

Sterile Lung Inflammation Induced by Silica Exacerbates Mycobacterium tuberculosis Infection via STING-Dependent Type 2 Immunity.

Lung inflammation induced by silica impairs host control of tuberculosis, yet the underlying mechanism remains unclear. Here, we show that silica-driven exacerbation of M. tuberculosis infection associates with raised type 2 immunity. Silica increases pulmonary Th2 cell and M2 macrophage responses, while reducing type 1 immunity after M. tuberculosis infection. Silica induces lung damage that prompts extracellular self-DNA release and activates STING. This STING priming potentiates M. tuberculosis DNA sensing by and activation of cGAS/STING, which triggers enhanced type I interferon (IFNI) response and type 2 immunity. cGAS-, STING-, and IFNAR-deficient mice are resistant to silica-induced exacerbation of M. tuberculosis infection. Thus, silica-induced self-DNA primes the host response to M. tuberculosis-derived nucleic acids, which increases type 2 immunity while reducing type 1 immunity, crucial for controlling M. tuberculosis infection. These data show how cGAS/STING pathway activation, at the crossroads of sterile inflammation and infection, may affect the host response to pathogens such as M. tuberculosis.