Miracle-dz/UniFAR-FTUs huggingface dataset:
The Integrated Role of Wnt/β-Catenin, N-Glycosylation, and E-Cadherin-Mediated Adhesion in Network Dynamics

The cellular network composed of the evolutionarily conserved metabolic pathways of protein N-glycosylation, Wnt/β-catenin signaling pathway, and E-cadherin-mediated cell-cell adhesion plays pivotal roles in determining the balance between cell proliferation and intercellular adhesion during development and in maintaining homeostasis in differentiated tissues. These pathways share a highly conserved regulatory molecule, β-catenin, which functions as both a structural component of E-cadherin junctions and as a co-transcriptional activator of the Wnt/β-catenin signaling pathway, whose target is the N-glycosylation-regulating gene, DPAGT1. Whereas these pathways have been studied independently, little is known about the dynamics of their interaction. Here we present the first numerical model of this network in MDCK cells. Since the network comprises a large number of molecules with varying cell context and time-dependent levels of expression, it can give rise to a wide range of plausible cellular states that are difficult to track. Using known kinetic parameters for individual reactions in the component pathways, we have developed a theoretical framework and gained new insights into cellular regulation of the network. Specifically, we developed a mathematical model to quantify the fold-change in concentration of any molecule included in the mathematical representation of the network in response to a simulated activation of the Wnt/ β-catenin pathway with Wnt3a under different conditions. We quantified the importance of protein N-glycosylation and synthesis of the DPAGT1 encoded enzyme, GPT, in determining the abundance of cytoplasmic β-catenin. We confirmed the role of axin in β-catenin degradation. Finally, our data suggest that cell-cell adhesion is insensitive to E-cadherin recycling in the cell. We validate the model by inhibiting β-catenin-mediated activation of DPAGT1 expression and predicting changes in cytoplasmic β-catenin concentration and stability of E-cadherin junctions in response to DPAGT1 inhibition. We show the impact of pathway dysregulation through measurements of cell migration in scratch-wound assays. Collectively, our results highlight the importance of numerical analyses of cellular networks dynamics to gain insights into physiological processes and potential design of therapeutic strategies to prevent epithelial cell invasion in cancer.
In vitro study of low intensity ultrasound combined with different doses of PDT: Effects on C6 glioma cells

The aim of this study was to study the effects of killing C6 glioma cells induced by hematoporphyrin monomethyl ether (HMME)-mediated sonodynamic therapy combined with photodynamic therapy (SPDT). In the SPDT group, the cells were treated with sonication at an intensity of 0.5 W/cm2 and a frequency of 1 MHz, followed by different doses of light irradiation. The growth inhibition rate following treatment was determined by MTT assay. The apoptotic rate was examined by a flow cytometry. Cleavage of caspase 3, 8 and 9 was investigated by immunoblotting. Reactive oxygen species (ROS) were measured by a fluorescence microplate reader. The effect of SPDT on the glioma cells was also studied in the absence or presence of various ROS scavengers. The growth inhibition rate of C6 glioma cells treated with SPDT was significantly higher compared with sonodynamic therapy (SDT) or photodynamic therapy (PDT) alone at light doses <200 J/cm2. The growth inhibition rate of C6 glioma cells treated with SPDT did not rise significantly when the light dose increased to >120 J/cm2. The apoptosis rate was the highest in the SPDT group, when the light dose was at 80 J/cm2. A greater amount of ROS were generated in the SPDT group than in the groups treated with SDT or PDT alone. The addition of NaN3 or mannitol resulted in a decrease in the growth inhibition rate with SPDT. In conclusion, our data indicate that SPDT powerfully kills C6 glioma cells in vitro through the synergistic effects of SDT and PDT. The pathway of PDT inducing C6 glioma cell apoptosis includes both the mitochondrial and death receptor pathways. Furthermore, ROS may play an important role in SPDT.
Phylogeography of Sulfate-Reducing Bacteria among Disturbed Sediments, Disclosed by Analysis of the Dissimilatory Sulfite Reductase Genes (dsrAB)

ABSTRACT Sediment samples were collected worldwide from 16 locations on four continents (in New York, California, New Jersey, Virginia, Puerto Rico, Venezuela, Italy, Latvia, and South Korea) to assess the extent of the diversity and the distribution patterns of sulfate-reducing bacteria (SRB) in contaminated sediments. The SRB communities were examined by terminal restriction fragment (TRF) length polymorphism (TRFLP) analysis of the dissimilatory sulfite reductase genes (dsrAB) with NdeII digests. The fingerprints of dsrAB genes contained a total of 369 fluorescent TRFs, of which <20% were present in the GenBank database. The global sulfidogenic communities appeared to be significantly different among the anthropogenically impacted (petroleum-contaminated) sites, but nearly all were less diverse than pristine habitats, such as mangroves. A global SRB indicator species of petroleum pollution was not identified. However, several dsrAB gene sequences corresponding to hydrocarbon-degrading isolates or consortium members were detected in geographically widely separated polluted sites. Finally, a cluster analysis of the TRFLP fingerprints indicated that many SRB microbial communities were most similar on the basis of close geographic proximity (tens of kilometers). Yet, on larger scales (hundreds to thousands of kilometers) SRB communities could cluster with geographically widely separated sites and not necessarily with the site with the closest proximity. These data demonstrate that SRB populations do not adhere to a biogeographic distribution pattern similar to that of larger eukaryotic organisms, with the greatest species diversity radiating from the Indo-Pacific region. Rather, a patchy SRB distribution is encountered, implying an initially uniform SRB community that has differentiated over time.
Computing Critical Pairs in Polygraphs

Polygraphs generalize to 2-categories the usual notion of equational theory, by describing them as quotients, modulo equations, of freely generated 2-categories on a given set of generators. In order to work with morphisms modulo the equations, it is often convenient to orient the equations into a confluent rewriting system. In the case of a terminating system, confluence can be checked by showing that critical pairs are joinable. However, the computation of the critical pairs is more complicated for polygraphs than for term rewriting systems: in particular, two left members of a rule don’t necessarily have a finite number of unifiers. We advocate here that a more general notion of rewriting system should be considered instead, and introduce an operad of compact contexts in a 2-category, in which two rules have a finite number of unifiers. A concrete representation of contexts is proposed, as well as an unification algorithm for these. ∗CEA LIST, Laboratory for the Modelling and Analysis of Interacting Systems, Point Courrier 94, 91191 Gif-sur-Yvette, France. E-mail: samuel.mimram@cea.fr. This work was started while I was in the PPS team (CNRS – Univ. Paris 7) and has been supported by the CHOCO (“Curry Howard pour la Concurrence”, ANR-07-BLAN-0324) and PANDA French ANRs.
Mutational specificity and genetic control of replicative bypass of an abasic site in yeast

Abasic (AP) sites represent one of the most frequently formed lesions in DNA, and they present a strong block to continued synthesis by the replicative DNA polymerases (Pols). Here we determine the mutational specificity and the genetic control of translesion synthesis (TLS) opposite an AP site in yeast by using a double-stranded plasmid system that we have devised in which bidirectional replication proceeds from a replication origin. We find that the rate, the genetic control, and the types and frequencies of nucleotides inserted opposite the AP site are very similar for both the leading and the lagging DNA strands, and that an A is predominantly inserted opposite the AP site, whereas C insertion by Rev1 constitutes a much less frequent event. In striking contrast, in studies that have been reported previously for AP bypass with gapped-duplex and single-stranded plasmids, it has been shown that a C is the predominant nucleotide inserted opposite the AP site. We discuss the implications of our observations for the mechanisms of TLS on the leading versus the lagging DNA strand and suggest that lesion bypass during replication involves the coordination of activities of the replicative Pol with that of the lesion-bypass Pol.
Evaluation of PFWD as potential quality control tool of pavement layers

Abstract Portable Falling Weight Deflectometer (PFWD) that can be considered as simple equipment is mainly used to measure elastic moduli of pavement unbound layers. This paper evaluates the potential use of PFWD to reliably measure the elastic modulus of pavement layers. To achieve this, PFWD tests were conducted on highway sections selected from different projects in Tehran. The California Bearing Ratio (CBR) laboratory tests were also conducted on samples collected during field tests. PFWD testing parameters were varied while performing the field testing. These included drop weight, drop height, plate diameter and position of additional geophones. In addition, PFWD moduli were compared with those obtained from performing FWD testing on the same site. It was found that drop mass and loading plate size affect PFWD modulus significantly. In addition, the results indicated that good correlation exist between PFWD moduli and FWD and CBR results.
Victor Ginsburgh DO MORE EXPENSIVE WINES TASTE BETTER ? EVIDENCE FROM A LARGE SAMPLE OF BLIND TASTINGS

Individuals who are unaware of the price do not derive more enjoyment from more expensive wine. In a sample of more than 6,000 blind tastings, we find that the correlation between price and overall rating is small and negative, suggesting that individuals on average enjoy more expensive wines slightly less. For individuals with wine training, however, we find indications of a positive relationship between price and enjoyment. Our results are robust to the inclusion of individual fixed effects, and are not driven by outliers: when omitting the top and bottom deciles of the price distribution, our qualitative results are strengthened, and the statistical significance is improved further. Our results indicate that both the prices of wines and wine recommendations by experts may be poor guides for non-expert wine consumers.
Total-energy study of electronic structure and mechanical behavior of C15 Laves phase compounds: NbCr2 and HfV2.

First-principles electronic structure calculations based on a full-potential linear muffin-tin orbital method have been used to study the electronic and mechanical properties of the early transition metal {ital C}15 Laves phase compounds NbCr{sub 2} and HfV{sub 2}. For both compounds, total energies are computed and compared for the two Laves phase crystal structures {ital C}15 and {ital C}14. The lower total-energy structure for NbCr{sub 2} is found to be the {ital C}15 structure as opposed to the {ital C}14 structure for HfV{sub 2}. We have calculated the equilibrium unit cell volumes, bulk moduli, cohesive energies, and heats of formation. We have obtained the density of states and charge density contour plots. Based on these results, we discuss the elastic properties, the stability of the {ital C}15 phase, and the bonding and deformation mechanisms in Laves phases. {copyright} {ital 1996 The American Physical Society. }
Long‐term in vitro analysis of limb cartilage development: Involvement of Wnt signaling

Endochondral skeletal development involves the condensation of mesenchymal cells, their differentiation into chondrocytes, followed by chondrocyte maturation, hypertrophy, and matrix mineralization, and replacement by osteoblasts. The Wnt family of secreted proteins have been shown to play important roles in vertebrate limb formation. To examine the role(s) of Wnt members and their transmembrane‐spanning receptor(s), Frizzled (fz), we retrovirally misexpressed Wnt‐5a, Wnt‐7a, chicken frizzled‐1 (Chfz‐1), and frizzled‐7 (Chfz‐7) in long‐term (21 day) high density, micromass cultures of stage 23/24 chick embryonic limb mesenchyme. This culture system recapitulates in vitro the entire differentiation (days 1–10), growth (days 5–12), and maturation and hypertrophy (from day 12 on) program of cartilage development. Wnt‐7a misexpression severely inhibited chondrogenesis from day 7 onward. Wnt‐5a misexpression resulted in a poor hypertrophic phenotype by day 14. Chfz‐7 misexpression caused a slight delay of chondrocyte maturation based on histology, whereas Chfz‐1 misexpression did not affect the chondrogenic phenotype. Misexpression of all Wnt members decreased collagen type X expression and alkaline phosphatase activity at day 21. Our findings implicate functional role(s) for Wnt signaling throughout embryonic cartilage development, and show the utility of the long‐term in vitro limb mesenchyme culture system for such studies. © 2004 Wiley‐Liss, Inc.
Osteomyelitis in the diabetic foot

Osteomyelitis (OM) is a common complication of diabetic foot ulcers and/or diabetic foot infections. This review article discusses the clinical presentation, diagnosis, and treatment of OM in the diabetic foot. Clinical features that point to the possibility of OM include the presence of exposed bone in the depth of a diabetic foot ulcer. Medical imaging studies include plain radiographs, magnetic resonance imaging, and bone scintigraphy. A high index of suspicion is also required to make the diagnosis of OM in the diabetic foot combined with clinical and radiological studies.
Difusion-Weighted MRI: from Brownian Motion to Head&Neck Tumor Characterization

This paper describes basic physics as well as clinical applications of diffusion-weighted magnetic resonance imaging. This is a technique that provides complementary information to conventional imaging sequences and it is applied in the field of oncologic imaging. This paper focuses on its specific application in head and neck, mainly in cancer patients, for characterization of primary tumors, and also for monitoring and predicting treatment response after chemotherapy or radiation therapy. Last, although diffusion-weighted imaging is shown to add value in several areas by being part of the multi-parametric magnetic resonance imaging approach, there are some unsolved challenges, which are proposed as future work.
Ranging With Ultrawide Bandwidth Signals in Multipath Environments

Over the coming decades, high-definition situationally-aware networks have the potential to create revolutionary applications in the social, scientific, commercial, and military sectors. Ultrawide bandwidth (UWB) technology is a viable candidate for enabling accurate localization capabilities through time-of-arrival (TOA)-based ranging techniques. These techniques exploit the fine delay resolution property of UWB signals by estimating the TOA of the first signal path. Exploiting the full capabilities of UWB TOA estimation can be challenging, especially when operating in harsh propagation environments, since the direct path may not exist or it may not be the strongest. In this paper, we first give an overview of ranging techniques together with the primary sources of TOA error (including propagation effects, clock drift, and interference). We then describe fundamental TOA bounds (such as the Cramer-Rao bound and the tighter Ziv-Zakai bound) in both ideal and multipath environments. These bounds serve as useful benchmarks in assessing the performance of TOA estimation techniques. We also explore practical low-complexity TOA estimation techniques and analyze their performance in the presence of multipath and interference using IEEE 802.15. 4a channel models as well as experimental data measured in indoor residential environments.
Over-imitation is better explained by norm learning than by distorted causal learning

In over-imitation, children copy even elements of a goal-directed action sequence that appear unnecessary for achieving the goal. We demonstrate in 4-year olds that the unnecessary action is specifically associated with the goal, not generally associated with the apparatus. The unnecessary action is performed flexibly: 4-year olds usually omit it if it has already been performed by an adult. Most 5-year olds do not verbally report the unnecessary action as necessary when achieving the goal, although most of them report an equivalent but necessary action as necessary. Most 5-year olds explain the necessary action in functional terms, but are unsure as to the function of the unnecessary action. These verbal measures do not support the hypothesis that children over-imitate primarily because they encode unnecessary actions as causing the goal even in causally transparent systems. In a causally transparent system, explanations for over-imitation fitting the results are that children are ignorant of the unnecessary action's purpose, and that they learn a prescriptive norm that it should be carried out. In causally opaque systems, however, for children and for adults, any action performed before achieving the goal is likely to be inferred as causally necessary—this is not over-imitation, but ordinary causal learning.
Raiders of the Lost Bark: Orangutan Foraging Strategies in a Degraded Landscape

Deforestation is rapidly transforming primary forests across the tropics into human-dominated landscapes. Consequently, conservationists need to understand how different taxa respond and adapt to these changes in order to develop appropriate management strategies. Our two year study seeks to determine how wild Sumatran orangutans (Pongo abelii) adapt to living in an isolated agroforest landscape by investigating the sex of crop-raiders related to population demographics, and their temporal variations in feeding behaviour and dietary composition. From focal animal sampling we found that nine identified females raided cultivated fruits more than the four males. Seasonal adaptations were shown through orangutan feeding habits that shifted from being predominantly fruit-based (56% of the total feeding time, then 22% on bark) to the fallback food of bark (44%, then 35% on fruits), when key cultivated resources such as jackfruit (Artocarpus integer), were unavailable. Cultivated fruits were mostly consumed in the afternoon and evening, when farmers had returned home. The finding that females take greater crop-raiding risks than males differs from previous human-primate conflict studies, probably because of the low risks associated (as farmers rarely retaliated) and low intraspecific competition between males. Thus, the behavioral ecology of orangutans living in this human-dominated landscape differs markedly from that in primary forest, where orangutans have a strictly wild food diet, even where primary rainforests directly borders farmland. The importance of wild food availability was clearly illustrated in this study with 21% of the total orangutan feeding time being allocated to feeding on cultivated fruits. As forests are increasingly converted to cultivation, humans and orangutans are predicted to come into conflict more frequently. This study reveals orangutan adaptations for coexisting with humans, e.g. changes in temporal foraging patterns, which should be used for guiding the development of specific human-wildlife conflict mitigation strategies to lessen future crop-raiding and conflicts.
Franklin Squares: A Chapter in the Scientific Studies of Magical Squares

Several aspects of magic(al) squares studies fall within the computational universe. Experimentalcomputationhasrevealed patterns, some ofwhich have lead to analytic insights, theorems, or combinatorial results. Other numerical experiments have provided statistical results for some very difficult problems. While classical nth order magic squares with the entries 1.n 2 must have the magic sum for each row, column, and the main diagonals, there are some interesting relatives for which these restrictions are increased or relaxed. These include: serial squares of all orders with sequential filling of rows which are always pandiagonal (i.e., having all parallel diagonals to the main ones on tiling with the same magic sum, also called broken diagonals); pandiagonallogic squares oforders 2 n derived from Karnaugh maps; Franklin squares of orders 8n which are not required to have any diagonal properties, but have equal half row and columnsums and 2-by-2 quartets; as well as sets of parallel magical bent diagonals. Our early explorations of magic squares, considered as square matrices, used Mathematica R to study their eigenproperties. We have also studied the moment of inertia and multipole moments of magic squares and cubes (treating the numerical entries as masses or charges), finding some elegant theorems. We have also shown how to easily compound smaller squares into very high order squares. There are patents proposing the use of magical squares for cryptography. Other possible applications include dither matrices for image processing and providing tests for developing constraint satisfaction problem (CSP) solvers for difficult problems.
Distributed Evolutionary Algorithm for Clustering Multi-Characteristic Social Networks

In this information era, data from different sources (online activities) are in abundance. Social media are increasingly providing activities and data, relations and interactions (audio, video and texting) among social actors (people), due to increasing capabilities of mobile devices and the ease access to the Internet. More than a billion people are now involved in online social media, and analyzing these interactive structures is a huge data-analytic problem. The primary focus of this work is to develop a clustering algorithm for multi-characteristic and dynamic online social networks. This work uses a combination of multi-objective evolutionary algorithms, distributed file systems and nested hybrid-indexing techniques to cluster the multi-characteristic dynamic social networks. Empirical results demonstrate that this adaptive clustering of dynamic social interactions can also provide a reliable distributed framework for BIG data analysis.