Miracle-dz/UniFAR-FTUs huggingface dataset:
Rôle des GTPases ARF dans la migration des cellules endothéliales et la sécrétion du NO

ARF6 and ARF1 are small GTPases of the ARF family(s) that regulate several signalling pathways including vesicles trafficking, lipid membrane remodelling and actin cytoskeleton reorganization. To date, the role of ARF6 and ARF1 in GPCR and RTK signalling, in endothelial cells, is little known. In this thesis, we aimed to characterize the role of ARF6 in the migration of endothelial cells induced by Enodothelin-1, and the role of ARF1 in the secretion of NO induced by VEGF. We show that ARF6 is essential for endothelial cell migration induced by endothelin-1. Inhibition of ARF6 expression using RNA interference markedly impaired basal and ET-1 stimulated cell migration. In this condition, FAK is found constitutively associated with Src. In contrast, depletion of ARF6 impairs the ability of GIT1 to form an agonist-promoted complex with FAK, thereby preventing disassembly of focal adhesions. As a consequence, adhesion of ARF6-depleted endothelial cells is increased and their motility is reduced. Furthermore, our result shows that ARF1 GTPase is essential for the activation of eNOS and the secretion of NO following VEGFR2 activation in endothelial cells. Inhibition of ARF1 expression using RNA interference markedly impaired the recruitment of Akt to the plasma membrane and its phosphorylation by the VEGF. As a consequence, the inhibition of Akt leads to an inhibition of eNOS, a well known downstream target, which in turn leads to inhibition of NO production. All together, our results indicate that ARF6 and ARF1 are essential for the ETB and the VEGFR2 signalling leading to cell migration and NO secretion respectively, two required steps for angiogenesis.
Study of a voltage-gated potassium channel in giant unilamellar vesicles

Il est difficile d'etudier in vivo le role de la membrane dans l'excitabilite des cellules car les parametres pertinents (composition et etat mecanique de la membrane, densite de canaux. . . ) sont activement regules par la cellule elle-meme et donc difficilement ajustables experimentalement. J’ai donc developpe une methode pour reconstituer un canal voltage-dependant dans une membrane ou ces parametres peuvent etre controles. Pour cela j’ai exprime, purifie et marque KvAP, un canal potassique voltage-dependant. J’ai ensuite adapte une methode existante pour le reconstituer dans des Vesicules Unilamellaires Geantes (GUVs). J’ai mesure la densite des canaux dans les GUVs grâce a la microscopie confocale. Des experiences d’electrophysiologie ont, de plus, montre que le canal reste fonctionnel apres reconstitution. Ce systeme m’a permis d’etudier tout d’abord l’affinite du canal pour les membranes courbees. Pour cela, j’ai tire des nanotubes de rayon controle a partir de ces GUVs et j’ai mesure la distribution du canal entre la vesicule et le tube par microscopie confocale. J’ai montre que le canal est enrichi dans le tube proportionnellement a sa courbure. Ce resultat est en accord avec une theorie basee sur l’elasticite de la membrane. Nous avons egalement etudie l’effet du confinement de la membrane sur la diffusion de KvAP. Par des experiences de suivi de particule unique, nous avons montre que le coefficient de diffusion le long du tube diminue d’un facteur 3 lorsque le rayon du tube decroit de 250 a 10 nm. Ce resultat est en accord avec le modele hydrodynamique de Saffman et Delbruck applique a la geometrie cylindrique
Phosphorus nutrition on nitrogen metabolism of non-nodulated soybean.

Two experiments were conducted under greenhouse conditions to study the influence of P deficiency on nitrogen nu - trition of non-nodulated soybean. There was a reduction of N and P content in P deficient (P-) plants of almost 50% after 50 days. During this period, dry matter of these plants was reduced by 33%. Nitrate reductase activity and shoot nitrate content were lower in P- than in P+ plants. Seventy five percent of nitrates in P- plants were in the roots. Nitrate accumulation in roots would be due to the lower nitrate reductase activity in this organ and a reduced water flux to shoots. Root nitrate concentration increases would cause a negative feedback which would reduce plant nitrate uptake.
Effects of water vapour pressure deficit on bulk canopy conductance in a beech forest

It is well known that turbulent water vapour ﬂuxes measured with closed-path eddy covariance (EC) systems can suffer from low pass ﬁltering by the system. The ﬂuxes are underestimated and need to be corrected. Recently it has been shown that the cut-off frequency of EC systems for water vapour concentration measurement is not a constant, but may increase exponentially with relative humidity, as an effect of water sorption and desorption on the surfaces of the EC-system (Ibrom et al. 2007). These effects must also lead to a cross-sensitivity between the ﬂux measurement and the water vapour pressure saturation deﬁcit ( D )
Le contexte archéologique des restes humains atériens de la région de Rabat-Témara (Maroc)

Depuis la fin des annees 50, la region de Rabat-Temara, sur le littoral atlantique marocain, a livre une serie de restes humains associes a un contexte archeologique aterien. L'apport principal de ces decouvertes fut de confirmer que l'auteur de la culture aterienne etait un Homo sapiens et non pas, comme cela avait ete suggere auparavant, un Homo neanderthalensis. Les restes humains, tous crâniens, associes a des niveaux contenant des industries ateriennes ont ete decouverts dans trois cavites : Dar-es-Soltane 2 (fouille A. Debenath), El Harhoura 1 (fouille A. Debenath) et Les Contrebandiers (fouille J. Roche). Dans ces grottes, les depots correspondants a l'Aterien sont caracterises par la faible densite de materiel archeologique qu'ils contiennent. La presence de pieces pedonculees fut un argument retenu pour l'attribution de ces niveaux a l'Aterien. Nous proposons ici une description et une analyse des documents disponibles sur les fouilles des annees 1970 et des donnees recemment acquises dans les grottes d'El Harhoura 2 et d'El Mnasra. Ces deux cavites apportent en effet d'importantes precisions sur les comportements humains. Les donnees fournies par les industries lithiques et les faunes chassees permettent de discuter de la presence aterienne, qui apparait comme une phase culturelle presentant la meme homogeneite que les restes humains s'y rapportant. La question des modalites et de l'intensite de l'occupation humaine durant le Paleolithique moyen dans cette region d'Afrique du Nord reste toutefois posee.
The Fluctuating enzyme

Free-Energy Management in Protein Reactions: Concepts, Complications, and Compensation (R. Lumry & R. B Gregory) The Statistical Nature of Protein Structural Fluctuations (A. Ikegami) The Statistical Time Correlation Approach to Enzyme Action: The Role of Hydration (G. Careri & E. Gratton) Molecular Dynamics and the Transient Strain Model of Enzyme Catalysis (B. Gavish) A Microenvironmental Approach to Enzyme Dynamics (B. Somogyi & S. Damjanovich) Processes of Conformational Relaxation in Enzyme Catalysis (L. A. Blumenfeld, D. S Burbajev & R. M Davydov) Electronic Conformational Interaction in Biopolymers (M. V. Volkenstein) Coherence and the Action of Enzymes (H. Frohlich) Not Just Catalysts--Molecular Machines in Bioenergetics (G. R. Welch & D. B Kell) Index.
Etude par simulations et calculs atomistiques, de la formation de dislocations aux défauts de surface dans un cristal de silicium soumis à des contraintes

Dans cette these, nous avons etudie au moyen de simulations atomistiques, la nucleation des dislocations a partir de marche de surface dans un cristal de silicium soumis a des contraintes. Afin de determiner le potentiel interatomique le mieux approprie a cette etude, nous avons compare les potentiels semi-empiriques de Stillinger-Weber (SW), Tersoff et EDIP avec des methodes ab initio sur des calculs de cisaillement homogene {111} du silicium massif, et d'energies de defauts d'empilement generalises sur les plans {111}. Les calculs ab initio montrent que la deformation se localise dans les plans du shuffle set, et pour de fortes deformations, les liaisons covalentes de ces plans deviennent metalliques. Pour notre etude, nous avons choisi le potentiel SW qui represente le mieux ces proprietes de cisaillement. A l'aide des potentiels interatomiques, principalement le potentiel SW, nous avons modelise un cristal de silicium comportant des marches de surface que nous avons soumis a diverses orientations de contraintes. Nous avons montre que les marches sont des sites privilegies pour l'initiation de la plasticite. L'analyse des deformations montre la nucleation de dislocations, en particulier de type 60°, qui ont glisse systematiquement dans des plans du shuffle set. De plus, le type de dislocation nucleee depend de la contrainte de scission resolue le long des plans de glissement et de la contrainte de Peierls. L'absence de cisaillement precurseur de la nucleation indique un couplage relativement faible entre tension et cisaillement des plans de glissement, contrairement aux metaux. Ce mecanisme de nucleation a ete valide par un calcul ab initio, ou une dislocation 60° a ete nucleee dans un plan du shuffle set. Cependant, l'activation de ces sources est difficile pour les marches de faible hauteur. Finalement, nous avons montre que les liaisons pendantes de surface facilitent la rupture/recombinaison des liaisons atomiques necessaires a la nucleation.
KRN5500, a Spicamycin Derivative, Exerts Anti-Myeloma Effects through Impairing Both Myeloma Cells and Osteoclasts.

Multiple myeloma (MM) is a plasma cell malignancy characterized by devastating bone destruction due to enhanced bone resorption and suppressed bone formation. Although high-dose chemotherapy and new agents such as thalidomide, lenalidomide, and bortezomib have shown marked anti-MM activity in clinical settings, MM remains incurable due to drug resistance mediated by interactions with osteoclasts or stroma cells. Moreover, osteolytic bone disease continues to be a major problem for many patients. Therefore, alternative approaches are necessary to overcome drug resistance and inhibit osteoclasts activity in MM. KRN5500 is a new derivative of spicamycin produced by Streptomyces alanosinicus (Kirin Pharma, Tokyo, Japan), which potently inhibits protein synthesis and induces cell death in human tumor cell lines. Phase I studies of KRN5500 in patients with solid tumors such as colon cancer and gastric cancer showed acceptable toxicity with Cmax values of 1000––3000 nM. In this study, we investigated the effects of KRN5500 against MM cells and osteoclasts in vitro and in vivo . MM cell lines such as RPMI 8226, MM.1S, INA-6, KMS12-BM, UTMC-2, TSPC-1, and OPC were incubated with various concentrations of KRN5500 for 3 days. Cell proliferation assay showed marked inhibition of cell growth with G1 arrest in these MM cells (IC50: 4–100 nM). KRN5500 (100 nM) also induced 30–90% of cell death in primary MM cells (n=7). Annexin V/propidium iodide staining showed that KRN5500 induced apoptosis of MM cells in a dose- and time-dependent manner. Western blot analysis confirmed activation of caspase-8, -9, and −3, cleavage of poly (ADP-ribose) polymerase (PARP), and down-regulation of Mcl-1. We next examined the effect of KRN5500 against MM cell lines and primary MM cells in the presence of bone marrow stroma cells and osteoclasts. Co-culture of these cells enhanced viability of MM cells; however, KRN5500 still induced strong cytotoxicity to MM cells. Of interest, KRN5500 specifically mediated apoptosis in osteoclasts but not stroma cells as assessed by TUNEL staining. More than 90% of osteoclasts were killed even at a low concentration of KRN5500 (20 nM). Finally, we evaluated the effect of KRN5500 against MM cells and osteoclasts in vivo . Two xenograft models were established in SCID mice by either subcutaneous injection of RPMI 8226 cells or intra-bone injection of INA-6 cells into subcutaneously implanted rabbit bones (SCID-rab model). These mice were treated with intraperitoneal injection of KRN5500 (5 mg/kg/dose) or saline thrice a week for 3 weeks after tumor development. In a subcutaneous tumor model, KRN5500 inhibited the tumor growth compared with control mice (increased tumor size, 232 ± 54% vs 950 ± 422%, p
Solids separation parameters for secondary clarifiers

Efficient separation of solids and supernatant is crucial in an activated‐sludge system because the performance of the system depends on the return of active biological solids to the biological reactor. For optimization and planning of the process, dynamic models describing the settling process are available. To use these models for simulations, parameters that characterize biomass settling must be known. The one‐dimensional model used in this work requires characteristic settling parameters from repeatedly performed batch tests. However, the model, together with its characteristic parameters, applies better to deep circular clarifiers than to rectangular ones. This work describes a new method to find the alternative settling parameters VA and nA, from dynamic measurements in a full‐scale rectangular clarifier, to be used for simulations of the same clarifier. Results from simulations of the movement of sludge blanket height in different clarifiers using the parameters VA and nA agreed well with full‐scale performance.
Hyper parameter estimation method with particle swarm optimization

Particle swarm optimization (PSO) method cannot be directly used in the problem of hyper-parameter estimation since the mathematical formulation of the mapping from hyper-parameters to loss function or generalization accuracy is unclear. Bayesian optimization (BO) framework is capable of converting the optimization of the hyper-parameters into the optimization of an acquisition function. The acquisition function is non-convex and multi-peak. So the problem can be better solved by the PSO. The proposed method in this paper uses the particle swarm method to optimize the acquisition function in the BO framework to get better hyper-parameters. The performances of proposed method in both of the classification and regression models are evaluated and demonstrated. The results on several benchmark problems are improved.
Geometrical dependence in Casimir-Polder repulsion

Repulsion, induced from quantum vacuum fluctuations, for an anisotropically polarizable atom on the symmetry axis of an anisotropically polarizable annular disc is studied. There exists two torsion free points on each side of the annular disc, where the interaction energy is orientation independent. The position of second of the two torsion free points, on either side of the disc, is shown to determine the orientation dependence of the atom at distances far from the plate, revealing a geometrical dependence. In the ring limit of the annular disc, new repulsion emerges.
Tensor Kernel Recovery for Discrete Spatio-Temporal Hawkes Processes

We introduce a new discrete spatio-temporal Hawkes process model by formulating the general influence of the Hawkes process as a tensor kernel. Based on the low-rank structure assumption of the tensor kernel, we cast the estimation of the tensor kernel as a convex optimization problem using the Fourier transformed nuclear norm. We provide theoretical performance guarantees for our approach and present an algorithm to solve the optimization problem. In particular, our upper bound of squared estimation error has the convergence rate of <inline-formula><tex-math notation="LaTeX">$O(lnK/\sqrt{K})$</tex-math></inline-formula>, where <inline-formula><tex-math notation="LaTeX">$K$</tex-math></inline-formula> is the number of samples in the time horizon. The efficiency of our estimation is demonstrated with numerical simulations on synthetic data and the analysis of real-world data from Atlanta burglary incidents.
Algorithms and Experiments Comparing Two Hierarchical Drawing Frameworks

We present algorithms that extend the path-based hierarchical drawing framework and give experimental results. Our algorithms run in $O(km)$ time, where $k$ is the number of paths and $m$ is the number of edges of the graph, and provide better upper bounds than the original path based framework: e.g., the height of the resulting drawings is equal to the length of the longest path of $G$, instead of $n-1$, where $n$ is the number of nodes. Additionally, we extend this framework, by bundling and drawing all the edges of the DAG in $O(m + n \log n)$ time, using minimum extra width per path. We also provide some comparison to a well known hierarchical drawing framework, widely known as the Sugiyama framework, as a proof of concept. The experimental results show that our algorithms produce drawings that are better in area and number of bends, but worse for crossings in sparse graphs. Hence, our technique offers an interesting alternative for drawing hierarchical graphs. Finally, we present an $O(m + k \log k)$ time algorithm that computes a specific order of the paths in order to reduce the total edge length and number of crossings and bends.
Viscous-like forces control the impact response of dense suspensions

We experimentally and theoretically study impacts into dense cornstarch and water suspensions. We vary impact speed as well as intruder size, shape, and mass, and we characterize the resulting dynamics using high-speed video and an onboard accelerometer. We numerically solve previously proposed models, most notably the added-mass model as well as a class of models where the viscous forces at the boundary of the jammed front are dominant. We find that our experimental data are inconsistent with the added mass model, but are consistent with the viscous model. Our results strongly suggest that the added-mass model, which is the dominant model for understanding the dynamics of impact into dense suspensions, should be updated to include these viscous-like forces.
Temporal Action Detection with Multi-level Supervision

Training temporal action detection in videos requires large amounts of labeled data, yet such annotation is expensive to collect. Incorporating unlabeled or weakly-labeled data to train action detection model could help reduce annotation cost. In this work, we first introduce the Semi-supervised Action Detection (SSAD) task with a mixture of labeled and unlabeled data and analyze different types of errors in the proposed SSAD baselines which are directly adapted from the semi-supervised classification literature. Identifying that the main source of error is action incompleteness (i.e., missing parts of actions), we alleviate it by designing an unsupervised foreground attention (UFA) module utilizing the conditional independence between foreground and background motion. Then we incorporate weakly-labeled data into SSAD and propose Omni-supervised Action Detection (OSAD) with three levels of supervision. To overcome the accompanying action-context confusion problem in OSAD baselines, an information bottleneck (IB) is designed to suppress the scene information in non-action frames while preserving the action information. We extensively benchmark against the baselines for SSAD and OSAD on our created data splits in THUMOS14 and ActivityNet1.2, and demonstrate the effectiveness of the proposed UFA and IB methods. Lastly, the benefit of our full OSAD-IB model under limited annotation budgets is shown by exploring the optimal annotation strategy for labeled, unlabeled and weakly-labeled data. 1
Matrix product states and projected entangled pair states: Concepts, symmetries, theorems

The theory of entanglement provides a fundamentally new language for describing interactions and correlations in many body systems. Its vocabulary consists of qubits and entangled pairs, and the syntax is provided by tensor networks. We review how matrix product states and projected entangled pair states describe many-body wavefunctions in terms of local tensors. These tensors express how the entanglement is routed, act as a novel type of non-local order parameter, and we describe how their symmetries are reflections of the global entanglement patterns in the full system. We will discuss how tensor networks enable the construction of real-space renormalization group flows and fixed points, and examine the entanglement structure of states exhibiting topological quantum order. Finally, we provide a summary of the mathematical results of matrix product states and projected entangled pair states, highlighting the fundamental theorem of matrix product vectors and its applications.
A Pattern-mining Driven Study on Differences of Newspapers in Expressing Temporal Information

This paper studies the differences between different types of newspapers in expressing temporal information, which is a topic that has not received much attention. Techniques from the fields of temporal processing and pattern mining are employed to investigate this topic. First, a corpus annotated with temporal information is created by the author. Then, sequences of temporal information tags mixed with part-of-speech tags are extracted from the corpus. The TKS algorithm is used to mine skip-gram patterns from the sequences. With these patterns, the signatures of the four newspapers are obtained. In order to make the signatures uniquely characterize the newspapers, we revise the signatures by removing reference patterns. Through examining the number of patterns in the signatures and revised signatures, the proportion of patterns containing temporal information tags and the specific patterns containing temporal information tags, it is found that newspapers differ in ways of expressing temporal information.
WeiPS: a symmetric fusion model framework for large-scale online learning

The recommendation system is an important commercial application of machine learning, where billions of feed views in the information flow every day. In reality, the interaction between user and item usually makes user's interest changing over time, thus many companies (e.g. ByteDance, Baidu, Alibaba, and Weibo) employ online learning as an effective way to quickly capture user interests. However, hundreds of billions of model parameters present online learning with challenges for real-time model deployment. Besides, model stability is another key point for online learning. To this end, we design and implement a symmetric fusion online learning system framework called WeiPS, which integrates model training and model inference. Specifically, WeiPS carries out second level model deployment by streaming update mechanism to satisfy the consistency requirement. Moreover, it uses multi-level fault tolerance and real-time domino degradation to achieve high availability requirement.
SUPPLEMENTAL INFORMATION: THE COMPLEXITY OF PROTEIN INTERACTIONS UNRAVELLED FROM STRUCTURAL DISORDER

We show different examples of the hierarchical organisation of the (very) different interfaces of clusters discussed in the main text. Firstly, we reproduce Fig 1 in a larger size in S1 Fig. We also show two additional examples, corresponding to clusters 3vd1_D in S2A Fig and 2c8g_A in S2B Fig. The different interfaces available but not included in the Figures were excluded either for lack of space, in the case of S1 Fig, or because they were very hard to distinguish by eye to one of the other interfaces shown in the tree.