Miracle-dz/UniFAR-FTUs huggingface dataset:
The lectin-like domain of thrombomodulin hampers host defence in pneumococcal pneumonia

The lectin-like domain of thrombomodulin (TM) plays an important regulatory role in sterile inflammatory conditions, but its role in severe Gram-positive infectious disease is unknown. Streptococcus pneumoniae is the most common cause of community-acquired pneumonia. The aim of this study was to determine the role of the lectin-like domain of TM in murine pneumococcal pneumonia. Wild-type (WT) mice and mice lacking the lectin-like domain of TM (TMLeD/LeD) were infected intranasally with viable S. pneumoniae and either observed in a survival study or euthanised 6, 24 or 48 h after infection. TMLeD/LeD mice had a markedly better survival in pneumococcal pneumonia when compared with WT mice. At 48 h post-infection with S. pneumoniae, TMLeD/LeD mice had lower bacterial loads in blood and liver, and exhibited less pulmonary inflammation, as shown by having less lung histopathology, less neutrophil influx and lower cytokine and chemokine levels. Plasma levels of pro-inflammatory cytokines were also reduced in TMLeD/LeD mice after exposure to the infection. Deletion of the lectin-like domain of TM improves the host defence in pneumococcal pneumonia. The lectin-like domain of TM may have a differential role in response to Gram-positive or Gram-negative bacteria.
THE SERUM BACTERICIDAL SYSTEM: ULTRASTRUCTURAL CHANGES IN NEISSERIA MENINGITIDIS EXPOSED TO NORMAL RAT SERUM

Exposure of meningococci to the bactericidal system of normal rat serum initiates a series of ultrastructural changes that accompany death of the organism. These morphological alterations consist of complement-dependent holes in the cell wall outer membrane, edema of the periplasmic space and cytoplasm, and accumulation of fibrillar material in and on the cell wall. Dissolution of the dense line and rupture of the cytoplasmic membrane also occur in meningococci exposed to normal rate serum. These latter two changes, however, are not seen in meningococci that are killed by bentonite-absorbed (lysozyme-deficient) serum, nor are they invariably present when other serum-susceptible organisms (N. catarrhalis and Herellea sp.) are treated with normal rat serum. The pattern of development of edema in serum-treated meningococci suggests that the cell wall outer membrane, mucopeptide layer, and cytoplasmic membrane act synergistically to maintain osmotic equilibrium of the bacterium. Death of the bacterium seems related to alteration of permeability following injury to the outer membrane. Holes are demonstrable, by negative straining, in the outer membrane of the meningococcal cell wall after exposure to the bactericidal effects of rat serum. The lesions are 110 A average greatest diameter and depend on the presence of antibody and complement for their formation. In addition, 82 A diameter holes are present in the walls of normal, untreated meningococci. The relation of complement-dependent holes to the smaller, naturally occurring holes is not known.
An adaptive graph model for automatic image annotation

Automatic keyword annotation is a promising solution to enable more effective image search by using keywords. In this paper, we propose a novel automatic image annotation method based on manifold ranking learning, in which the visual and textual information are well integrated. Due to complex and unbalanced data distribution and limited prior information in practice, we design two new schemes to make manifold ranking efficient for image annotation. Firstly, we design a new scheme named the Nearest Spanning Chain (NSC) to generate an adaptive similarity graph, which is robust across data distribution and easy to implement. Secondly, the word-to-word correlations obtained from WordNet and the pairwise co-occurrence are taken into consideration to expand the annotations and prune irrelevant annotations for each image. Experiments conducted on standard Corel dataset and web image dataset demonstrate the effectiveness and efficiency of the proposed method for image annotation.
Hierarchical streamline bundles for visualizing 2D flow fields.

We present hierarchical streamline bundles, a new approach to simplifying and visualizing 2D flow fields. Our method first densely seeds a flow field and produces a large number of streamlines that capture important flow features such as critical points. Then, we group spatially neighboring and geometrically similar streamlines to construct a hierarchy from which we extract streamline bundles at different levels of detail. Streamline bundles highlight multiscale flow features and patterns through a clustered yet non-cluttered display. This selective visualization strategy effectively accentuates visual foci and therefore is able to convey the desired insight into the flow fields. The hierarchical streamline bundles we have introduced offer a new way to characterize and visualize the flow structure and patterns in multiscale fashion. Streamline bundles highlight critical points clearly and concisely. Exploring the hierarchy allows a complete visualization of important flow features. Thanks to selective streamline display and flexible LOD refinement, our multiresolution technique is scalable and is promising for viewing large and complex flow fields. In the future, we would like to seek a cost-effective way to generate streamlines without enforcing the dense seeding condition. We will also extend this approach to handle real-world 3D complex flow fields.
Fast Recurrent Fully Convolutional Networks for Direct Perception in Autonomous Driving

Deep convolutional neural networks (CNNs) have been shown to perform extremely well at a variety of tasks including subtasks of autonomous driving such as image segmentation and object classification. However, networks designed for these tasks typically require vast quantities of training data and long training periods to converge. We investigate the design rationale behind end-to-end driving network designs by proposing and comparing three small and computationally inexpensive deep end-to-end neural network models that generate driving control signals directly from input images. In contrast to prior work that segments the autonomous driving task, our models take on a novel approach to the autonomous driving problem by utilizing deep and thin Fully Convolutional Nets (FCNs) with recurrent neural nets and low parameter counts to tackle a complex end-to-end regression task predicting both steering and acceleration commands. In addition, we include layers optimized for classification to allow the networks to implicitly learn image semantics. We show that the resulting networks use 3x fewer parameters than the most recent comparable end-to-end driving network and 500x fewer parameters than the AlexNet variations and converge both faster and to lower losses while maintaining robustness against overfitting.
Priming with an Adenovirus 35-Circumsporozoite Protein (CS) Vaccine followed by RTS,S/AS01B Boosting Significantly Improves Immunogenicity to Plasmodium falciparum CS Compared to That with Either Malaria Vaccine Alone

ABSTRACT The RTS,S/AS02A protein-based vaccine consistently demonstrates significant protection against infection with Plasmodium falciparum malaria and also against clinical malaria and severe disease in children in areas of endemicity. Here we demonstrate with rhesus macaques that priming with a replication-defective human adenovirus serotype 35 (Ad35) vector encoding circumsporozoite protein (CS) (Ad35.CS), followed by boosting with RTS,S in an improved MPL- and QS21-based adjuvant formulation, AS01B, maintains antibody responses and dramatically increases levels of T cells producing gamma interferon and other Th1 cytokines in response to CS peptides. The increased T-cell responses induced by the combination of Ad35.CS and RTS,S/AS01B are sustained for at least 6 months postvaccination and may translate to improved and more durable protection against P. falciparum infection in humans.
The SAMI Galaxy Survey: global stellar populations on the size–mass plane

We present an analysis of the global stellar populations of galaxies in the SAMI (Sydney-AAO Multi-object Integral field spectrograph) Galaxy Survey. Our sample consists of 1319 galaxies spanning four orders of magnitude in stellar mass and includes all morphologies and environments. We derive luminosity-weighted, single stellar population equivalent stellar ages, metallicities and alpha enhancements from spectra integrated within one effective radius apertures. Variations in galaxy size explain the majority of the scatter in the age–mass and metallicity–mass relations. Stellar populations vary systematically in the plane of galaxy size and stellar mass, such that galaxies with high stellar surface mass density are older, more metal rich and alpha enhanced than less dense galaxies. Galaxies with high surface mass densities have a very narrow range of metallicities; however, at fixed mass, the spread in metallicity increases substantially with increasing galaxy size (decreasing density). We identify residual correlations with morphology and environment. At fixed mass and size, galaxies with late-type morphologies, small bulges and low Sersic n are younger than early type, high n, high bulge-to-total galaxies. Both age and metallicity show small residual correlations with environment; at fixed mass and size, galaxies in denser environments or more massive haloes are older and somewhat more metal rich than those in less dense environments. We connect these trends to evolutionary tracks within the size–mass plane.
PARAMETRIC STUDY ON AN ACTIVE COMPRESSION BANDAGE PERFORMANCE

ABSTRACT Smart materials such as shape memory alloys have intrigued the scientific community for decades. They exhibit mechanical properties that other, more conventional alloys do not as they can undergo super-elasticity. Namely, this paper is focused on analyzing the performance of an active compression bandage (ACB) analytically. This ACB, which is capable of actively applying an altering external pressure on the lower limbs, has been prototyped using smart alloy technology. The ACB actuated by shape memory alloy (SMA) wires was designed and prototyped for potentially being used in future clinical studies to prevent or mitigate symptoms of lower extremity disorders. The prototyped ACB can apply an initial compression comparable to the one applied by commercial compression stockings by wrapping around the patient’s calf. Then the pressure can be increased based on the activation of the shape memory alloys by running current through them. In this work, a parametric study was conducted using a previously developed analytical model of the bandage based on a shape memory alloy constitutive model. This study evaluates the performance of the bandage for different diameters and numbers of wires, as well as the initial wrapping pressure. Results show a significant increase of actuation pressure due to an increase in the number of SMA wires for the same amount of applied electrical current. Furthermore, the initial pressure can have an effect on the actuation pressure after the martensite phase transformation. A larger diameter of the SMA wires results in a larger actuation pressure and also increases the required electrical current for starting the martensite to austenite phase transformation.
CEA LIST's participation to the Scalable Concept Image Annotation task of ImageCLEF 2015

This paper describes our participation to the ImageCLEF 2015 scalable concept image annotation task. Our system is only based on visual features extracted with a deep Convolutional Neural Network (CNN). The network is trained with noisy web data corresponding to the concepts to detect in this task. We introduce a simple concept localization pipeline that provides the localization of the detected concepts, among the 251 concepts, within the images.
Irradiation damage of oxide dispersion strengthened steels

Advanced fission and fusion power offer long-term energy production from fundamentally carbon-free fuel sources, with high-energy densities and high reliability. However, for these power sources to be realised, many materials challenges need to be addressed. Oxide dispersion strengthened (ODS) ferritic alloys are recognized as potential fission fuel cladding and fusion structural materials because of their high-temperature stability and swelling-resistance imparted by the nano-scale oxide clusters they contain. This work presents the study of a set of model ODS alloys with a systematic variation in alloy chemistry in order to investigate the influence of chemical additions on the oxide cluster nature and the irradiation resistance. To investigate these properties, the high-resolution characterisation techniques of atom probe tomography and transmission electron microscopy were applied in combination with nanoindentation to assess mechanical properties and X-ray diffraction to study the crystallinity. The quantification of the character of the oxide particles in these ODS alloys by atom probe tomography presented a number of challenges and I extend the conventional analysis techniques in order to overcome these difficulties. By comparison of the addition of Ti, and then Cr, to a Fe-Y 2 O 3 alloy, the influence of alloy chemistry on the oxide particles was evaluated. The main aims were to investigate the microstructure, the oxide cluster composition and to set a baseline to which the irradiated samples were compared. The irradiation damage of the oxide clusters was investigated using ion irradiation as an analogue for neutron damage. Irradiation experiments were performed at a range of temperatures and the stability of the clusters was assessed based on their size, number density and chemistry. Subtle changes in cluster chemistry at elevated temperatures and the dramatic changes which occurred after irradiation at low temperatures lead to conclusions about the competition of thermal diffusion and irradiation damage.
Identification of Turbostratic Bilayer Grephene in Carbon Tribolayers

It is expected that friction forces should cause drastic changes in the structure of rubbed off trace of sp2 bulk graphite (carbon tribolayer or CTL). In this work we studied some properties of CTL. It is found that CTL contains segments of different transmission of light unique to carbon allotropes different from sp2. X-ray diffraction (XRD) pattern, optical absorption spectra reveal a sp2 crystalline structure on the surface of CTL. The Raman spectrum shows distinguished and narrow peaks with symmetrical line shape. Intensity ratio of 2D and G peaks is close to 1 which is characteristic of two-layer graphene. Increased interlayers pacing measured by XRD as well as symmetry of 2D peak of Raman spectra testifies to the presence of turbostratic two-layer sp2 phase at the surface of CTL.
Requirements for Measles Virus Induction of RANTES Chemokine in Human Astrocytoma-Derived U373 Cells

ABSTRACT Interferons and chemokines play a critical role in regulating the host response to viral infection. Measles virus, a member of theParamyxoviridae family, induces RANTES expression by astrocytes. We have examined the mechanism of this induction in U373 cells derived from a human astrocytoma. RANTES was induced in a dose- and time-dependent manner by measles virus infection. Inhibition of receptor binding by the anti-CD46 antibody TRA-2.10 and of virus-membrane fusion by the tripeptide X-Phe-Phe-Gly reduced RANTES expression. Formalin-inactivated virus, which can bind but not fuse, and extensively UV-irradiated virus, which can bind and fuse, were both ineffective. Therefore, virus binding to the cellular receptor CD46 and subsequent membrane fusion were necessary, but not sufficient, to induce RANTES. UV irradiation of virus for less than 10 min proportionally inhibited viral transcription and RANTES expression. RANTES induction was decreased in infected cells treated with ribavirin, which inhibits measles virus transcription. However, RANTES mRNA was superinduced by measles virus in the presence of cycloheximide. These data suggest that partial transcription of the viral genome is sufficient and necessary for RANTES induction, whereas viral protein synthesis and replication are not required. This hypothesis was supported by the fact that RANTES was induced through transient expression of the measles virus nucleocapsid gene but not by measles genes encoding P or L proteins or by leader RNA in A549 cells. Thus, transcription of specific portions of measles virus RNA, such as the nucleocapsid gene, appears able to generate the specific signaling required to induce RANTES gene expression.
Stochastic geometry and random graphs for the analysis and design of wireless networks

Wireless networks are fundamentally limited by the intensity of the received signals and by their interference. Since both of these quantities depend on the spatial location of the nodes, mathematical techniques have been developed in the last decade to provide communication-theoretic results accounting for the networks geometrical configuration. Often, the location of the nodes in the network can be modeled as random, following for example a Poisson point process. In this case, different techniques based on stochastic geometry and the theory of random geometric graphs -including point process theory, percolation theory, and probabilistic combinatorics-have led to results on the connectivity, the capacity, the outage probability, and other fundamental limits of wireless networks. This tutorial article surveys some of these techniques, discusses their application to model wireless networks, and presents some of the main results that have appeared in the literature. It also serves as an introduction to the field for the other papers in this special issue.
Identification of monosomy 3 in choroidal melanoma by chromosome in situ hybridisation

Background/aims: In uveal melanoma monosomy 3 is emerging as a significant indicator of a poor prognosis. To date most cytogenetic studies of uveal melanoma have utilised fresh tissue or DNA extracted from tissue sections. In this study chromosome in situ hybridisation (CISH) was used to study monosomy 3 in tissue sections. The copy number of chromosome 3 was determined and related to patient survival. Methods: Archival glutaraldehyde or formalin fixed, paraffin embedded material was obtained from 30 metastasising and 26 non-metastasising choroidal melanomas. Hybridisations were performed using centromere specific probes to chromosomes 3 and 18. Chromosome 18 was included as a control as previous abnormalities in uveal melanoma have not been described. Chromosomal imbalance was defined on the basis of changes in both chromosome index and signal distribution. Results: CISH was successfully performed on both glutaraldehyde and formalin fixed tissue. Four cases were unsuccessful because of extensive tumour necrosis. All cases were balanced for chromosome 18. Monosomy 3 was detected in 15 of the 26 cases of metastasising melanoma; the 26 non-metastasising tumours were all balanced for chromosome 3. Monosomy 3 was significantly associated with metastases related death. Conclusion: CISH can successfully identify monosomy 3 in archival glutaraldehyde or formalin fixed, paraffin embedded tissue sections. Similar to previous studies monosomy 3 is a significant predictor of metastases related death.
DEVS modeling and simulation based on Markov Decision Process of financial leverage effect in the EU development programs

The evaluation of development programs has become essential to verify their success. Indeed, it is necessary to develop prediction tools of the still-planned programs, in a special phase called ex-ante phase, to simulate the effects of fictitious programs or changes in the existing program structure in order to predict the level of leverage of a program from its design stage as well as during the project. The proposed paper consists of the definition of a DEVS-based Markov Decision Process model which, after simulation, may constitute an ex-ante evaluation of a development program. First promising simulation results are presented and seems to confirm the right way of the proposed approach.
Genetic variants in GCKR and PNPLA3 confer susceptibility to nonalcoholic fatty liver disease in obese individuals.

BACKGROUND A genome-wide association study identified variants in or near patatin-like phospholipase domain-containing-3 (PNPLA3), neurocan (NCAN), lysophospholipase-like 1 (LYPLAL1), glucokinase regulatory protein (GCKR), and protein phosphatase 1 regulatory subunit 3b (PPP1R3B) that were strongly associated with nonalcoholic fatty liver disease (NAFLD) in adults of European ancestry. OBJECTIVE We examined these genetic variants in obese children and tested whether their effects on NAFLD are significant in the Taiwanese Han Chinese population. DESIGN We genotyped PNPLA3 rs738409, NCAN rs2228603, LYPLAL1 rs12137855, GCKR rs780094, and PPP1R3B rs4240624 in 797 obese children aged 7-18 y. NAFLD was identified by liver ultrasonography. We analyzed the effect of these genetic variants on NAFLD. RESULTS NAFLD was identified in 24% of the recruited obese children. We found significant associations with NAFLD at variants in PNPLA3 and GCKR but not in NCAN, LYPLAL1, and PPP1R3B. Multiple logistic regression analysis showed that, after control for the effects of age- and sex-adjusted body mass index, waist-to-hip ratio, sex, and PNPLA3 rs738409 polymorphism, the variant GCKR rs780094 TT genotype independently increased the OR of NAFLD by 1.997 (95% CI: 1.196, 3.335; P = 0.008) compared with the CC genotype. Subjects with the variant GCKR rs780094 TT genotype had a higher mean serum alanine aminotransferase concentration than did those with the CC genotype (30.8 ± 34.7 compared with 22.2 ± 18.6 IU/L; P = 0.01). CONCLUSIONS By studying the genetic variants of obese Taiwanese children, we confirmed that the genetic variants in GCKR rs780094 and PNPLA3 rs738409, but not in NCAN rs2228603, LYPLAL1 rs12137855, and PPP1R3B rs4240624, are associated with an increased risk of NAFLD. GCKR and PNPLA3 variants are the common genetic factors that may confer susceptibility to NAFLD in obese individuals across multiple ethnic groups.
End-to-end tracing considered essential

Concurrency and complexity are major obstacles to understanding application performance in high-performance systems. We advocate end-to-end event tracing as the correct way to expose performance information for both human and automated analysis. We describe its advantages over traditional performance counter data, and illustrate its uses in performance visualization, prediction for capacity planning, and anomaly detection. We conclude with a look at opportunities and challenges presented by a widespread deployment of end-to-end tracing.