pinecone/core-2020-05-10-deduplication huggingface dataset:
CTCF-mediated transcriptional regulation through cell type-specific chromosome organization in the β-globin locus.

International audienceThe principles underlying the architectural landscape of chromatin beyond the nucleosome level in living cells remains largely unknown despite its potential to play a role in mammalian gene regulation. We investigated the three-dimensional folding of a 1 Mbp region of human chromosome 11 containing the β-globin genes by integrating looping interactions of the CCCTC-binding insulator protein CTCF determined comprehensively by chromosome conformation capture (3C) into a polymer model of chromatin. We find that CTCF-mediated cell type-specific interactions in erythroid cells are organized to favor contacts known to occur in vivo between the β-globin locus control region (LCR) and genes. In these cells, the modeled β-globin domain folds into a globule with the LCR and the active globin genes on the periphery. In contrast, in non-erythroid cells, the globule is less compact with few but dominant CTCF interactions driving the genes away from the LCR. This leads to a decrease in contact frequencies that can exceed 1000-fold depending on the stiffness of the chromatin and the exact position of the genes. Our findings show that an ensemble of CTCF contacts functionally affects spatial distances between control elements and target genes contributing to chromosomal organization required for transcription
Environmental quality, public debt and economic development

International audienceThis article analyzes the consequences on capital accumulation and environmental quality of environmental policies financed by public debt. A public sector of pollution abatement is financed by a tax and/or public debt. We show that if the initial capital stock is high enough, the economy monotonically converges to a long-run steady state. On the contrary, when the initial capital stock is low, the economy is relegated to an environmental-poverty trap. We also explore the implications of public policies on the trap and on the long-run stable steady state. In particular, we find that government should decrease debt and increase pollution abatement to promote capital accumulation and environmental quality at the stable long-run steady state
Combining Language Models with NLP and Interactive Query Expansion.

International audienceFollowing our previous participation in INEX 2008 Ad-hoc track, we continue to address both standard and focused retrieval tasks based on comprehensible language models and interactive query expansion (IQE). Query topics are expanded using an initial set of Multiword Terms (MWTs) selected from top n ranked documents. In this experiment, we extract MWTs from article titles, narrative field and automatically generated summaries. We combined the initial set of MWTs obtained in an IQE process with automatic query expansion (AQE) using language models and smoothing mechanism. We chose as baseline the Indri IR engine based on the language model using Dirichlet smoothing. We also compare the performance of bag of word approaches (TFIDF and BM25) to search strategies elaborated using language model and query expansion (QE). The experiment is carried out on all INEX 2009 Ad-hoc tasks
Concretizing the Process Hitting into Biological Regulatory Networks

Accepted at the conference CMSB 2012. http://sites.brunel.ac.uk/cmsb2012International audienceThe Process Hitting (PH) is a recently introduced framework to model concurrent processes. Its major originality lies in a specific restriction on the causality of actions, which makes the formal analysis of very large systems tractable. PH is suitable to model Biological Regulatory Networks (BRNs) with complete or partial knowledge of cooperations between regulators by defining the most permissive dynamics with respect to these constraints. On the other hand, the qualitative modeling of BRNs has been widely addressed using René Thomas' formalism, leading to numerous theoretical work and practical tools to understand emerging behaviors. Given a PH model of a BRN, we first tackle the inference of the underlying Interaction Graph between components. Then the inference of corresponding Thomas' models is provided using Answer Set Programming, which allows notably an efficient enumeration of (possibly numerous) compatible parametrizations. In addition to giving a formal link between different approaches for qualitative BRNs modeling, this work emphasizes the ability of PH to deal with large BRNs with incomplete knowledge on cooperations, where Thomas' approach fails because of the combinatorics of parameters
Foundation, analysis, and numerical investigation of a variational network-based model for rubber

International audienceSince the pioneering work by Treloar, many models based on polymer chain statistics have been proposed to describe rubber elasticity. Recently, Alicandro, Cicalese, and the first author have rigorously derived a continuum theory of rubber elasticity from a discrete model by variational convergence. The aim of this paper is twofold. First we further physically motivate this model, and complete the analysis by numerical simulations. Second, in order to compare this model to the literature, we present in a common language two other representative types of models, specify their underlying assumptions, check their mathematical properties, and compare them to Treloar's experiments
From the onset of damage to rupture: construction of responses with damage localization for a general class of gradient damage models

International audienceWe propose a construction method of non homogeneous solutions for the traction problem of an elastic damaging bar. This bar has a softening behavior which obeys a gradient damaged model. The method is applicable for a wide range of brittle materials. For sufficiently long bars, we show that localization arises on sets whose length is proportional to the material internal length and with a profile which is also a material characteristic. From its onset until the rupture, the damage profile is obtained either in a closed form or after a simple numerical integration depending on the model. Thus, the proposed method provides definitions for the critical stress and fracture energy that can be compared with experimental results. We finally discuss some features of the global behavior of the bar such as the possibility of a snap-back at the onset of damage. We point out the sensitivity of the responses to the parameters of the damage law. All these theoretical considerations are illustrated by numerical examples
Some convergence results for Howard's algorithm

International audienceThis paper deals with convergence results of Howard's algorithm for the resolution of $\min_{a\in \cA} (B^a x - b^a)=0$ where $B^a$ is a matrix, $b^a$ is a vector (possibly of infinite dimension), and $\cA$ is a compact set. We show a global super-linear convergence result, under a monotonicity assumption on the matrices $B^a$. In the particular case of an obstacle problem of the form $\min(A x - b,\, x-g)=0$ where $A$ is an $N\times N$ matrix satisfying a monotonicity assumption, we show the convergence of Howard's algorithm in no more than $N$ iterations, instead of the usual $2^N$ bound. Still in the case of obstacle problem, we establish the equivalence between Howard's algorithm and a primal-dual active set algorithm (M. Hintermüller et al., {\em SIAM J. Optim.}, Vol 13, 2002, pp. 865-888). We also propose an Howard-type algorithm for a "double-obstacle" problem of the form $\max(\min(Ax-b,x-g),x-h)=0$. We finally illustrate the algorithms on the discretization of nonlinear PDE's arising in the context of mathematical finance (American option, and Merton's portfolio problem), and for the double-obstacle problem
Modeling of vine agronomic practices in the context of climate change

International audienceGlobal climate change affects regional climates and hold implications for viticulture worldwide. Many studies have addressed the issue of the impact of climate change on viticulture in most wine regions worldwide, yet few studies are devoted to observing and simulating both climate and climate change at the "terroir" scale (local scale). However, phenological variations as well as differences in grapes/wine quality are often observed over short distances in a wine-region, which are related to local characteristics (slope, soil, seasonal climate . . .). This paper proposes a modeling approach to simulate behavior changes in wine grower activities and to analyze the impact of changing strategies in wine production. Two experiments were conducted in the small wine appellation grand cru Quart de Chaume (Coteaux du Layon, Loire Valley, France) and in the wine estate in Mendoza (Bodega Alta Vista) where all of the methodology (from the implementation of the knowledge database to the analysis of the first simulation) is presented. Given that this prototype is still under development, several research perspectives are discussed
Coefficients of different macro-microscopic mass formulae from the AME2012 atomic mass evaluation

The coefficients of different possible macro-microscopic mass formulae previously proposed have been adjusted on 2264 experimental atomic masses extracted from the AME2012 atomic mass evaluation [1] assuming N,Z⩾8 and the one standard deviation uncertainty on the mass lower than 150 keV. All the formulae include the volume and surface energies, the Coulomb energy, the diffuseness correction to the sharp radius Coulomb energy, the shell and pairing energies and take into account or not the curvature energy, different forms of the Wigner term, a free charge radius, the experimental equivalent rms charge radius or a fixed short central radius. Masses of 976 more exotic nuclei are extrapolated from the most accurate formula
Plate motions, Andean orogeny, and volcanism above the South Atlantic convection cell

International audienceThe geometric and kinematic evolution of the Andes provides insight onto the nature of the force balance beneath the South American plate. While the Andean load is opposed on its western edge by the force induced by subduction of the Nazca plate, its more elusive eastern counterpart, which we explore herein, requires some contribution from the mantle beneath the South Atlantic. Using a mantle flow model, we show that the Andes owe their existence to basal drag beneath South America caused by a cylindrical convection cell under the South Atlantic. We find that the observed Andean uplift requires both westward push fromactive upwelling beneath Africa andwestward drag toward the downgoing Nazca slab. These mutually-reinforcing downwellings and upwellings amount to 38% and 23% of the total driving force, respectively. Further decomposition reveals that the South Atlantic cell is most vigorous near its center, rendering the net drag force higher where the Andes also reach their highest elevation. Kinematic reconstructions suggest that the South Atlantic cell could have grown owing to the migration of the Nazca slab until ~50 Ma. We propose that from 50 Ma onwards, the cell may have ceased growing westward because (i) it had reached an optimal aspect ratio and (ii) the Nazca slab became anchored into the lower mantle. Continued westward motion of the plates, however, moved the surface expressions of spreading and convergence away from the upwelling and downwelling arms of this cell. Evidence for this scenario comes from the coeval tectonic, morphologic, and magmatic events in Africa and South America during the Tertiary
Learning to trade in an unbalanced market

We study the evolution of trading strategies in double auctions as the size of the market gets larger. When the number of buyers and sellers is balanced, Fano et al.~(2011) show that the choice of the order-clearing rule (simultaneous or asynchronous) steers the emergence of fundamentally different strategic behavior. We extend their work to unbalanced markets, confirming their main result as well as that allocative inefficiency tends to zero. On the other hand, we discover that convergence to the competitive outcome takes place only when the market is large and that the long side of the market is more effective at improving its disadvantaged terms of trade under asynchronous order-clearing
Occurrence and distribution of glycerol dialkyl glycerol tetraethers in a French peat bog

International audienceThe present study was aimed at examining the distribution and abundance of glycerol dialkyl glycerol tetraethers (GDGTs) of archaeal and bacterial origin in peat samples from surface and deep (ca. 50 cm) horizons of a peat bog in the Jura Mountains (northeastern France). Two principal types of GDGTs are present: extractable GDGTs, recoverable by solvent extraction, and non-extractable GDGTs, linked to the soil matrix. Within the extractable pool, “free” (i.e. core lipids) and “bound” (i.e. intact polar and/or ester-bound lipids) GDGTs can be distinguished. Extractable “free” and “bound” GDGTs were extracted using both accelerated solvent extraction (ASE) and a modified Bligh and Dyer technique. Both methods were shown to allow adequate extraction of “free” archaeal and bacterial GDGTs from soil samples. Both extraction protocols afforded similar relative distributions of archaeal and bacterial GDGTs, although poorer extraction of “bound” GDGTs was observed for ASE relative to Bligh and Dyer. Even though only low amounts of bacterial GDGTs were released after acid hydrolysis of solvent-extracted samples, non-extractable and total extractable GDGTs showed different distribution patterns in some samples. Consequently, these two lipid pools potentially reflect different proxy records of mean annual air temperature (MAAT) and pH. Last, the distribution of bacterial GDGTs differed between the different samples. Samples from deep horizons gave lower GDGT-derived MAAT values than those from surficial horizons, in agreement with measured soil temperatures at 7 cm and 50 cm depths from April to September. MAAT estimates more closely resemble spring and summer temperatures rather than annual soil temperature. The variability in bacterial GDGT distribution and resulting MAAT estimates probably also reflects the heterogeneity of peat samples and the variation in several environmental factors such as peat moisture level and oxygen availability
Near-field interactions between a subwavelength tip and a small-volume photonic-crystal nanocavity

International audienceThe fundamentals of the near-field interaction between a subwavelength metallic tip and a photonic-crystal nanocavity are investigated experimentally and theoretically. It is shown experimentally that the cavity resonance is tuned without any degradation by the presence of the tip and that the reported near-field interaction is strongly related to the field distribution within the nanostructure. Then, in light of a perturbation theory, we show that this interaction is selectively related to the electric field or magnetic field distribution within the cavity, depending on the tip properties
Muscarinic M2 acetylcholine receptor distribution in the guinea-pig gastrointestinal tract

In the enteric nervous system, acetylcholine is the most common neurotransmitter to induce gastrointestinal smooth muscle contractions. Cholinergic signaling is mediated by muscarinic acetylcholine receptors on the surface of smooth muscle cells. Five different muscarinic receptor subtypes (M1–M5) have been identified and characterized, all of which belong to the superfamily of the G-protein-coupled receptor. The muscarinic M2 acetylcholine receptor is the major muscarinic receptor subtype expressed by smooth muscle tissues in the gastrointestinal tract, where it is coexpressed with a smaller population of M3 receptor. In this study, we examined the immunohistochemical distribution of the M2 receptor using a specific antibody in the guinea-pig gastrointestinal tract. M2 receptor-like immunoreactivity was mainly observed as associated with smooth muscle cells in the gastrointestinal tract. M2 receptor-like immunoreactivity in smooth muscle cells was distributed throughout the cell membrane associated with caveolae. In the proximal colon, M2 receptor-like immunoreactivity in the smooth muscle cells was weak. In the small intestine, interstitial cells of Cajal that possessed neurokinin 1 receptor-like immunoreactivity had intense M2 receptor-like immunoreactivity. In the proximal colon, intramuscular and myenteric interstitial cells of Cajal exhibited M2 receptor-like immunoreactivity. These findings indicate that, in the gastrointestinal musculature, M2 receptors are distributed both in the smooth muscle cells and interstitial cells of Cajal, suggesting that the M2 receptor elicits smooth muscle cell contraction and the interstitial cells of Cajal are the sites of innervation by enteric cholinergic neurons
Influence of aspirin therapy in the ulcer associated with chronic venous insufficiency

Producción CientíficaBackground: To determine the effect of aspirin on ulcer healing rate in patients with chronic
venous insufficiency, and to establish prognostic factors that influence ulcer evolution.
Methods: Between 2001 and 2005, 78 patients with ulcerated lesions of diameter >2 cm and
associated with chronic venous insufficiency were evaluated in our hospital. Of these, 51 patients
(22 men, 29 women) with mean age of 60 years (range: 36e86) were included in a prospective
randomized trial with a parallel control group. The treatment group received 300 mg of aspirin and
the control group received no drug treatment; in both groups, healing was associated with standard
compression therapy. During follow-up, held weekly in a blinded fashion, there was ulcer
healing as well as cases of recurrence. Results were analyzed by intention-to-treat approach.
Cure rate was estimated using KaplaneMeir survival analysis, and the influence of prognostic
factors was analyzed by applying the Cox proportional hazards model.
Results: In the presence of gradual compression therapy, healing occurred more rapidly in
patients receiving aspirin versus the control subjects (12 weeks in the treated group vs. 22
weeks in the control group), with a 46% reduction in healing time. The main prognostic factor
was estimated initial area of injury (P ¼ 0.032). Age, sex, systemic therapy, and infection
showed little relevance to evolution.
Conclusions: The administration of aspirin daily dose of 300 mg shortens the healing time of
ulcerated lesions in the chronic venous insufficiency (CVI). The main prognostic factor for healing
of venous ulcerated lesions is the initial surface area of the ulcer
Loss of Nephrocystin-3 Function Can Cause Embryonic Lethality, Meckel-Gruber-like Syndrome, Situs Inversus, and Renal-Hepatic-Pancreatic Dysplasia

Many genetic diseases have been linked to the dysfunction of primary cilia, which occur nearly ubiquitously in the body and act as solitary cellular mechanosensory organelles. The list of clinical manifestations and affected tissues in cilia-related disorders (ciliopathies) such as nephronophthisis is broad and has been attributed to the wide expression pattern of ciliary proteins. However, little is known about the molecular mechanisms leading to this dramatic diversity of phenotypes. We recently reported hypomorphic NPHP3 mutations in children and young adults with isolated nephronophthisis and associated hepatic fibrosis or tapetoretinal degeneration. Here, we chose a combinatorial approach in mice and humans to define the phenotypic spectrum of NPHP3/Nphp3 mutations and the role of the nephrocystin-3 protein. We demonstrate that the pcy mutation generates a hypomorphic Nphp3 allele that is responsible for the cystic kidney disease phenotype, whereas complete loss of Nphp3 function results in situs inversus, congenital heart defects, and embryonic lethality in mice. In humans, we show that NPHP3 mutations can cause a broad clinical spectrum of early embryonic patterning defects comprising situs inversus, polydactyly, central nervous system malformations, structural heart defects, preauricular fistulas, and a wide range of congenital anomalies of the kidney and urinary tract (CAKUT). On the functional level, we show that nephrocystin-3 directly interacts with inversin and can inhibit like inversin canonical Wnt signaling, whereas nephrocystin-3 deficiency leads in Xenopus laevis to typical planar cell polarity defects, suggesting a role in the control of canonical and noncanonical (planar cell polarity) Wnt signaling
Application of Membrane Inlet Mass Spectrometry for Online and In Situ Analysis of Methane in Aquatic Environments

A method is presented for the online measurement of methane in aquatic environments by application of membrane inlet mass spectrometry (MIMS). For this purpose, the underwater mass spectrometer Inspectr200-200 was applied. A simple and reliable volumetric calibration technique, based on the mixing of two end member concentrations, was used for the analysis of CH4 by MIMS. To minimize interferences caused by the high water vapor content, permeating through the membrane inlet system into the vacuum section of the mass spectrometer, a cool-trap was designed. With the application of the cool-trap, the detection limit was lowered from 100 to 16 nmol/L CH4. This allows for measurements of methane concentrations in surface and bottom waters of coastal areas and lakes. Furthermore, in case of membrane rupture, the cool-trap acts as a security system, avoiding total damage of the mass spectrometer by flushing it with water. The Inspectr200-200 was applied for studies of methane and carbon dioxide concentrations in coastal areas of the Baltic Sea and Lake Constance. The low detection limit and fast response time of the MIMS allowed a detailed investigation of methane concentrations in the vicinity of gas seepages
Infection of Anopheles gambiae mosquitoes with entomopathogenic fungi: effect of host age and blood-feeding status.

Physiological characteristics of insects can influence their susceptibility to fungal infection of which age and nutritional status are among the most important. An understanding of host-pathogen interaction with respect to these physiological characteristics of the host is essential if we are to develop fungal formulations capable of reducing malaria transmission under field conditions. Here, two independent bioassays were conducted to study the effect of age and blood-feeding status on fungal infection and survival of Anopheles gambiae s.s. Giles. Mosquitoes were exposed to 2 × 10(10) conidia m(-2) of oil-formulated Metarhizium anisopliae ICIPE-30 and of Beauveria bassiana I93-825, respectively, and their survival was monitored daily. Three age groups of mosquitoes were exposed, 2-4, 5-8, and 9-12 days since emergence. Five groups of different feeding status were exposed: non-blood-fed, 3, 12, 36, and 72 h post-blood feeding. Fungal infection reduced the survival of mosquitoes regardless of their age and blood-feeding status. Although older mosquitoes died relatively earlier than younger ones, age did not tend to affect mosquito susceptibility to fungal infection. Non-blood-fed mosquitoes were more susceptible to fungus infection compared to all categories of blood-fed mosquitoes, except for those exposed to B. bassiana 72 h post-blood feeding. In conclusion, formulations of M. anisopliae and B. bassiana can equally affect mosquitoes of different age classes, with them being relatively more susceptible to fungus infection when non-blood-fed