Miracle-dz/UniFAR-FTUs huggingface dataset:
Membrane insertion: The strategies of toxins (review).

Protein toxins are soluble molecules secreted by pathogenic bacteria which act at the plasma membrane or in the cytoplasm of target cells. They must therefore interact with a membrane at some point, either to modify its permeability properties or to reach the cytoplasm. As a consequence, toxins have the built-in capacity to adopt two generally incompatible states: water-soluble and transmembrane. Irrespective of their origin or function, the membrane interacting domain of most protein toxins seems to have adopted one out of two structural strategies to be able to undergo this metamorphosis. In the first group of toxins the membrane interacting domain has the structural characteristics of most known membrane proteins, i.e. it contains hydrophobic and amphipathic alpha-helices long enough to span a membrane. To render this 'membrane protein' water-soluble during the initial part of its life the hydrophobic helices are sheltered from the solvent by a barrel of amphipathic helices. In the second group of toxins the opposite strategy is adopted. The toxin is an intrinsically soluble protein and is composed mainly of beta-structure. These toxins manage to become membrane proteins by oligomerizing in order to combine amphipathic beta-sheet to generate sufficient hydrophobicity for membrane insertion to occur. Toxins from this latter group are thought to perforate the lipid bilayer as a beta-barrel such as has been described for bacterial porins, and has recently been shown for staphylococcal alpha-toxin. The two groups of toxins will be described in detail through the presentation of examples. Particular attention will be given to the beta-structure toxins, since four new structures have been solved over the past year: the staphyloccocal alpha-toxin channel, the anthrax protective antigen protoxin, the anthrax protective antigen-soluble heptamer and the CytB protoxin. Structural similarities with mammalian proteins implicated in the immune response and apoptosis will be discussed. Peptide toxins will not be covered in this review.
A bioactive hybrid three-dimensional tissue-engineering construct for cartilage repair

The aim was to develop a hybrid three-dimensional-tissue engineering construct for chondrogenesis. The hypothesis was that they support chondrogenesis. A biodegradable, highly porous polycaprolactone-grate was produced by solid freeform fabrication. The polycaprolactone support was coated with a chitosan/polyethylene oxide nanofibre sheet produced by electrospinning. Transforming growth factor-β3-induced chondrogenesis was followed using the following markers: sex determining region Y/-box 9, runt-related transcription factor 2 and collagen II and X in quantitative real-time polymerase chain reaction, histology and immunostaining. A polycaprolactone-grate and an optimized chitosan/polyethylene oxide nanofibre sheet supported cellular aggregation, chondrogenesis and matrix formation. In tissue engineering constructs, the sheets were seeded first with mesenchymal stem cells and then piled up according to the lasagne principle. The advantages of such a construct are (1) the cells do not need to migrate to the tissue engineering construct and therefore pore size and interconnectivity problems are omitted and (2) the cell-tight nanofibre sheet and collagen-fibre network mimic a cell culture platform for mesenchymal stem cells/chondrocytes (preventing escape) and hinders in-growth of fibroblasts and fibrous scarring (preventing capture). This allows time for the slowly progressing, multiphase true cartilage regeneration.
Multi-level Revenue Sharing for Viral Marketing

In this paper we present the design and analysis of revenue sharing schemes for viral marketing over social networks. The increasing need for monetizing social networks more effectively is causing social network platforms to look for alternatives to online behavioral targeting. Specifically, we turn to cooperative game theory and the Shapley value to design revenue sharing schemes to incentivize users to help the social network platform for more effective viral marketing. Our goal is to identify mechanisms that achieve desirable objectives in terms of computability, individual rationality, and potential reach. In particular, we propose multi-level revenue sharing for referral-based and viral marketing over online social networks. We show via simulations that users have more incentive to collaborate with the social network platform in implementing the campaign when the revenue or discount is shared across multiple levels rather than the commonly used single-level model. For this purpose, we design the graph-based model, for which we show that computing the Shapley value is #P-hard. However, we show that in a variation of that model, which we call the tree-based model, computing the Shapley value becomes polynomial time. We also show that the revenue function is supermodular only in the tree-based model. Supermodularity of the revenue function entails desirable corollaries.
8-D reflectance field for computational photography

Some computational photography techniques have been proposed to control the focus and illumination of captured images. However, the relationship between the techniques have been unclear because they were developed independently for different purposes. In this research we propose a unified framework to explain the computational photography techniques in the computation of an 8-D reflectance field. Moreover, for an 8-D reflectance field we show that the synthetic aperture, the image-based relighting, and the confocal imaging techniques can be realized using the same measuring device.
Semantic types: a fresh look at the ideal model for types

We present a generalization of the ideal model for recursive polymorphic types. Types are defined as sets of terms instead of sets of elements of a semantic domain. Our proof of the existence of types (computed by fixpoint of a typing operator) does not rely on metric properties, but on the fact that the identity is the limit of a sequence of projection terms. This establishes a connection with the work of Pitts on relational properties of domains. This also suggests that ideals are better understood as closed sets of terms defined by orthogonality with respect to a set of contexts.
A constrained spectral inversion method based on compressive sensing in order to distinguish high-quality shale

Multi-wave exploration has become one of the main means of unconventional shale gas exploration in the Sichuan Basin, China. How to effectively improve the resolution of the shale gas reservoir layer and distinguish high-quality shale has become one of the difficulties for shale gas exploration. The spectral inversion technology can effectively break the resolution limit of the conventional technology and greatly improve the resolution of the thin shale layer; however, it also needs enough prior information to overcome the problem of multiple solutions in the inversion. The compressed sensing (CS) theory has the ability to reconstruct complete data using incomplete data can use less data information to improve the accuracy of spectral inversion. A novel constrained spectral inversion method based on CS is presented to handle these situations. The CS technique is applied to the objective function of spectral inversion, which can improve the accuracy of the spectral inversion algorithm and create profiles with a higher resolution and greater continuity. Applications through theoretical and real data can illustrate very high performance of the presented algorithm. Distinguishing high-quality shale effectively is a difficult exploration problem. We propose a constrained spectral inversion method based on compressive sensing to handle this challenge. This method can help us improve the resolution and continuity of the profiles and enhance our ability to discover high-quality shale.
Cloning of Salmonella enterica Serovar Enteritidis Fimbrial Protein SefA as a Surface Protein in Escherichia coli Confers the Ability To Attach to Eukaryotic Cell Lines

ABSTRACT The gene for the Salmonella enterica serovar Enteritidis fimbrial protein SefA was cloned into an Escherichia coli surface expression vector and confirmed by Western blot assay. E. coli clones expressing SefA attached to avian ovary granulosa cells and HEp-2 cells, providing evidence for the involvement of SefA in the ability of Salmonella to attach to eukaryotic cells.
Extending the Modified Bayesian Information Criterion (mBIC) to Dense Markers and Multiple Interval Mapping

Summary The modified version of Bayesian Information Criterion (mBIC) is a relatively simple model selection procedure that can be used when locating multiple interacting quantitative trait loci (QTL). Our earlier work demonstrated the statistical properties of mBIC for situations where the average genetic map interval is at least 5 cM. In this work mBIC is adapted to genome searches based on a dense map and, more importantly, to the situation where consecutive QTL and interactions are located by multiple interval mapping. Easy to use formulas for the extended mBIC are given. A simulation study, as well as the analysis of real data, confirm the good properties of the extended mBIC.
Field trials of a telephone service for rail travel information

This paper reports on the RAILTEL field trial carried out by LIMSI, to assess the technical adequacy of available speech technology for interactive vocal access to static train timetable information. The data collection system used to carry out the field trials, is based on the LIMSI MASK spoken language system and runs on a Unix workstation with a high quality telephone interface. The spoken language system allows a mixed-initiative dialog where the user can provide any information at any point in time. Experienced users are thus able to provide all the information needed for database access in a single sentence, whereas less experienced users tend to provide shorter responses, allowing the system to guide them. The RAILTEL field trial was carried out using a commonly defined upon methodology. 100 naive subjects participated in the field trials, each contributing one call and completing a user questionnaire. 72% of the callers successfully completed their scenarios. The subjective assessment of the service was for the most part favorable, with subjects expressing interest in using such a service.
Cooperative Beamforming for a Two-Cell System with Limited Feedback

In this paper we investigate a two-cell downlink scenario with base station cooperation. We assume that a limited amount of feedback for channel state information (CSI) is available and optimize the numbers of bits for quantizing the desired and interfering channels. A cooperative beamforming strategy with limited feedback is proposed which selects suitable beamforming schemes from zero forcing (ZF) and eigen-beamforming based on the received interference and noise power level of the users. It is shown that the proposed cooperative strategy outperforms existing schemes in different interference scenarios.
A phase-field model of stress effect on grain boundary migration

We developed a phase-field model to study the stress-driven grain boundary migration in elastically inhomogeneous polycrystalline materials with arbitrary elastic inhomogeneity and anisotropy. The dependence of elastic stiffness tensor on grain orientation is taken into account, and the elastic equilibrium equation is solved using the Fourier spectral iterative-perturbation method. We studied the migration of planar and curved grain boundaries under an applied stress. The relation between grain boundary migration velocity and driving force is found to be linear in the steady-state regime. Our study shows that the stress distribution depends on the relative misorientation between the grains and the nature of the applied load. As a consequence, the mechanism of grain boundary migration is different when the load is applied parallel or perpendicular to a grain boundary. The bulk mechanical driving force for grain boundary migration is provided by the difference in the level of stress in the adjoining grains which arise due to difference in elastic moduli. We further show that under certain conditions an applied stress may act as a precursor to abnormal grain growth.
Doppler ultrasonographic evaluation of splanchnic blood flow in coeliac disease.

BACKGROUND: Current knowledge on splanchnic haemodynamics in coeliac disease is limited and incomplete. AIM: To evaluate splanchnic arterial and venous blood flow in coeliac disease. METHODS: In 22 coeliac (13 untreated, nine treated) patients and in nine healthy subjects the following variables were assessed: vessel diameter and mean flow velocity in portal vein, splenic vein, superior mesenteric vein, and superior mesenteric artery. Peak systolic velocity, end diastolic velocity and pulsatility index were also determined in the superior mesenteric artery. Five patients of the untreated group were re-evaluated after nine months on a gluten free diet. RESULTS: Significant differences in haemodynamic variables between the three groups were shown only in the superior mesenteric artery. An increase in both mean flow velocity and end diastolic velocity and a reduction in pulsatility index occurred in untreated patients compared with treated patients (p < 0.002; p < 0.04; p < 0.035) and with healthy controls (p < 0.001; p < 0.025; p < 0.0003). Similar results were obtained for the five patients evaluated before and after treatment (p < 0.03; p < 0.02; p < 0.03), in whom the mean flow velocity in the superior mesenteric vein also decreased after treatment (p < 0.05). No significant differences were noted between treated coeliac patients and healthy controls. CONCLUSIONS: In untreated coeliac disease there is a hyperdynamic mesenteric circulation that decreases after treatment.
SST: An algorithm for searching sequence databases in time proportional to the logarithm of the database size

W e have developed an algorithm, called SST (Sequence Search T that searches database of DNA sequences for near exact matches, in time proportional to the logarithm of the database size n. In SST, we partition each sequence into fragments of fixed length called "windows" using multiple offsets. Each window is mapped into a vector of dimension 4 k which contains the frequency of occurrence of its component k-tuples, with k a parameter typically in the range 4 6. Then we create a tree-structured index of the windows in vector space, using tree structured vector quantization (TSVW e identify the nearest-neighbors of a query sequence by partitioning the query into windows and searching the tree-structured index for nearest neighbor windows in the database. This yields an O(log n) complexity for the search. SST is most effective for applications in which the target sequences show a high degree of similarity to the query sequence, such as assembling shotgun sequences or matching ESTs to genomic sequence. The algorithm is also an effective filtration method. Specifically , it can be used as a preprocessing step for other search methods to reduce the complexity of searching one large database against another. F or the problem of identifying overlapping fragments in the assembly of 120,000 fragments from a 1.5 megabase genomic sequence, SST is 17 to 35 times faster than BLAST when we consider both building and searching the tree. F or searching alone (i.e., after building the tree SST is 50 to 100 times faster than BLAST.
Hilbert transformer and time delay: statistical comparison in the presence of Gaussian noise

We have shown that in the presence of independent and identically distributed (i.i.d.) additive Gaussian noise, the performance of a time delay as a phase shifter, which produces a signal-dependent phase shift, is comparable with the performance of a Hilbert transformer which produces a signal-independent 90/spl deg/ phase shift, especially for high signal-to-noise ratios (SNRs) and the proper choice of the delay. Sinusoidal signals are considered. It is shown that the time-delay phase process in Gaussian noise can be approximated by the noise-free phase plus a non-Gaussian phase noise. As the SNR increases, the expected value of the time-delay phase estimator approaches the true value of the phase, and its variance substantially decreases and converges to the Cramer-Rao bound for all ranges of the effective parameters: the phase shift, the deterministic phase, and SNR. A symmetric transformation of the phase probability density function (PDF) that improves the performance of the time delay in Gaussian noise is also proposed.
First Human Model of In Vitro Candida albicans Persistence within Granuloma for the Reliable Study of Host-Fungi Interactions

Backgound The balance between human innate immune system and Candida albicans virulence signaling mechanisms ultimately dictates the outcome of fungal invasiveness and its pathology. To better understand the pathophysiology and to identify fungal virulence-associated factors in the context of persistence in humans, complex models are indispensable. Although fungal virulence factors have been extensively studied in vitro and in vivo using different immune cell subsets and cell lines, it is unclear how C. albicans survives inside complex tissue granulomas. Methodology/Principal Finding We developed an original model of in vitro human granuloma, reproducing the natural granulomatous response to C. albicans. Persistent granulomas were obtained when the ratio of phagocytes to fungi was high. This in vitro fungal granuloma mimics natural granulomas, with infected macrophages surrounded by helper and cytotoxic T lymphocytes. A small proportion of granulomas exhibited C. albicans hyphae. Histological and time-lapse analysis showed that C. albicans blastoconidia were located within the granulomas before hyphae formation. Using staining techniques, fungal load calculations, as well as confocal and scanning electron microscopy, we describe the kinetics of fungal granuloma formation. We provide the first direct evidence that C. albicans are not eliminated by immunocompetent cells inside in vitro human granulomas. In fact, after an initial candicidal period, the remaining yeast proliferate and persist under very complex immune responses. Conclusions/Significance Using an original in vitro model of human fungal granuloma, we herein present the evidence that C. albicans persist and grow into immunocompetent granulomatous structures. These results will guide us towards a better understanding of fungal invasiveness and, henceforth, will also help in the development of better strategies for its control in human physiological conditions.
A 36nV/√Hz noise PSD chopper-stabilized CMOS amplifier with a new ripple-spur-filter scheme

A low-noise, low-power CMOS amplifier is developed using the chopper-stabilized technique. A new filter scheme is employed to suppress chopping ripple and spur. It composes of a band-pass amplifier, a novel low-pass-chopper (LPC) and a low-pass class-AB output stage. With the LPC, the amplifier rejects unexpected high frequency signal by about extra -12dB, which shares burden of the band-pass amplifier. The proposed amplifier is simulated in TSMC 0.35-μm CMOS process and a noise PSD of 36nV/√Hz and a unity gain bandwidth of 1MHz with an overall current consumption of 14. 5μA are achieved.
On a certain generalization of spherical twists

This note gives a generalization of spherical twists, and describe the autoequivalences associated to certain non-spherical objects. Typically these are ob- tained by deforming the structure sheaves of (0; 2)-curves on threefolds, or deforming P-objects introduced by D. Huybrechts and R. Thomas. Resume (Sur une generalisation des twists spheriques). — Cette note donne une generalisation des twists spheriques et decrit des auto-equivalences associees a certains objets qui ne sont pas spheriques. Typiquement ces objets sont obtenus par deformation du faisceau structural d'une (0;2)-courbe dans une variete de dimension trois ou d'un P-objet introduit par D. Huybrechts et R. Thomas.
Pathological features and inhaled corticosteroid response of eosinophilic and non-eosinophilic asthma

Background: Non-eosinophilic asthma is a potentially important clinicopathological phenotype since there is evidence that it responds poorly to inhaled corticosteroid therapy. However, little is known about the underlying airway immunopathology and there are no data from placebo-controlled studies examining the effect of inhaled corticosteroids. Methods: Airway immunopathology was investigated using induced sputum, bronchial biopsies, bronchial wash and bronchoalveolar lavage in 12 patients with symptomatic eosinophilic asthma, 11 patients with non-eosinophilic asthma and 10 healthy controls. The patients with non-eosinophilic asthma and 6 different patients with eosinophilic asthma entered a randomised, double-blind, placebo-controlled crossover study in which the effects of inhaled mometasone 400 μg once daily for 8 weeks on airway responsiveness and asthma quality of life were investigated. Results: Patients with non-eosinophilic asthma had absence of eosinophils in the mucosa (median 4.4 cells/mm2 vs 23 cells/mm2 in eosinophilic asthma and 0 cells/mm2 in normal controls; p = 0.03) and normal subepithelial layer thickness (5.8 μm vs 10.3 μm in eosinophilic asthma and 5.1 μm in controls, p = 0.002). Non-eosinophilic and eosinophilic asthma groups had increased mast cell numbers in the airway smooth muscle compared with normal controls (9 vs 8 vs 0 cells/mm2, p = 0.016). Compared with placebo, 8 weeks of treatment with inhaled mometasone led to less improvement in methacholine PC20 (0.5 vs 5.5 doubling concentrations, 95% CI of difference 1.1 to 9.1; p = 0.018) and asthma quality of life (0.2 vs 1.0 points, 95% CI of difference 0.27 to 1.43; p = 0.008). Conclusions: Non-eosinophilic asthma represents a pathologically distinct disease phenotype which is characterised by the absence of airway eosinophilia, normal subepithelial layer thickness and a poor short-term response to treatment with inhaled corticosteroids.
The chondrocyte, architect of cartilage. Biomechanics, structure, function and molecular biology of cartilage matrix macromolecules

Chondrocytes are specialised cells which produce and maintain the extracellular matrix of cartilage, a tissue that is resilient and pliant. In vivo, it has to withstand very high compressive loads, and that is explicable in terms of the physico‐chemical properties of cartilage‐specific macromolecules and with the movement of water and ions within the matrix. The functions of the cartilage‐specific collagens, aggrecan (a hydrophilic proteoglycan) and hyaluronan are discussed within this context. The structures of cartilage collagens and proteoglycans and their genes are known and a number of informative mutations have been identified. In particular, collagen fibrillogenesis is a complex process which can be altered by mutations whose effects fit what is known about collagen molecular structural functions. In other instances, mutations have indicated new functions for particular molecular domains. As cartilage provides the template for the developing skeleton, mutations in genes for cartilage‐specific proteins often produce developmental abnormalities. The search for mutations amongst such genes in heritable disorders is being actively pursued by many groups, although mutation and phenotype are not always well correlated, probably because of compensatory mechanisms. The special nature of the chondrocyte is stressed in connection with its cell involvement in osteoarthritis, the most widespread disease of diarthrodial joints.