Miracle-dz/UniFAR-FTUs huggingface dataset:
TLR3 Increases Disease Morbidity and Mortality from Vaccinia Infection1

Innate immunity is required for effective control of poxvirus infections, but cellular receptors that initiate the host response to these DNA viruses remain poorly defined. Given this information and the fact that functions of TLRs in immunity to DNA viruses remain controversial, we investigated effects of TLR3 on pathogenesis of vaccinia virus, a prototype poxvirus. We used a recombinant strain Western Reserve vaccinia virus that expresses firefly luciferase to infect wild-type C57BL/6 and TLR3−/− mice through intranasal inoculation. Bioluminescence imaging showed that TLR3−/− mice had substantially lower viral replication in the respiratory tract and diminished dissemination of virus to abdominal organs. Mice lacking TLR3 had reduced disease morbidity, as measured by decreased weight loss and hypothermia after infection. Importantly, TLR3−/− mice also had improved survival relative to wild-type mice. Infected TLR3−/− mice had significantly reduced lung inflammation and recruitment of leukocytes to the lung. Mice lacking TLR3 also had lower levels of inflammatory cytokines, including IL-6, MCP-1, and TNF-α in serum and/or bronchoalveolar lavage fluid, but levels of IFN-β did not differ between genotypes of mice. To our knowledge, our findings show for the first time that interactions between TLR3 and vaccinia increase viral replication and contribute to detrimental effects of the host immune response to poxviruses.
A Bayesian mixture model for multi-view face alignment

For multi-view face alignment, we have to deal with two major problems: 1) the problem of multi-modality caused by diverse shape variation when the view changes dramatically; 2) the varying number of feature points caused by self-occlusion. Previous works have used nonlinear models or view based methods for multi-view face alignment. However, they either assume all feature points are visible or apply a set of discrete models separately without a uniform criterion. In this paper, we propose a unified framework to solve the problem of multi-view face alignment, in which, both the multi-modality and variable feature points are modeled by a Bayesian mixture model. We first develop a mixture model to describe the shape distribution and the feature point visibility, and then use an efficient EM algorithm to estimate the model parameters and the regularized shape. We use a set of experiments on several datasets to demonstrate the improvement of our method over traditional methods.
CRMP2 Tethers Kainate Receptor Activity to Cytoskeleton Dynamics during Neuronal Maturation

The CRMP2 and CRMP4 proteins are strongly expressed in the developing nervous system, mediating neurite outgrowth, neuronal polarity, and axon guidance. In the present study, we demonstrate the interaction of the CRMP2 and CRMP4 proteins with the GluK5 subunit of the kainate (KA) receptor (KAR) and investigated the role of KARs in modulating the development of cultured mouse DRG neurons. We found that KARs modulate neuronal maturation and neurite outgrowth in a bidirectional manner. Accordingly, low concentrations of KA delayed maturation and enhanced neurite outgrowth, whereas maturation was promoted by higher concentrations of KA that attenuated neuritic elongation. The effects of weak KAR activation were prevented by blocking their noncanonical signaling and involved a differential regulation of CRMP2. Whereas the delay in maturation involves PKC-mediated phosphorylation of CRMP2 at T555 leading to a downregulation of membrane Cav2.2, the promotion of neurite outgrowth is achieved by dephosphorylation at T514 at the growth cones, the latter reflecting PKC-driven enhancement of GSK3β phosphorylation at S9. Together, these findings indicate that noncanonical KAR signaling influences neuronal development by modulating CRMP2 activity.
Metagenomic Analyses of the Autotrophic Fe(II)-Oxidizing, Nitrate-Reducing Enrichment Culture KS

ABSTRACT Nitrate-dependent ferrous iron [Fe(II)] oxidation (NDFO) is a well-recognized chemolithotrophic pathway in anoxic sediments. The neutrophilic chemolithoautotrophic enrichment culture KS originally obtained from a freshwater sediment (K. L. Straub, M. Benz, B. Schink, and F. Widdel, Appl Environ Microbiol 62:1458–1460, 1996) has been used as a model system to study NDFO. However, the primary Fe(II) oxidizer in this culture has not been isolated, despite extensive efforts to do so. Here, we present a metagenomic analysis of this enrichment culture in order to gain insight into electron transfer pathways and the roles of different bacteria in the culture. We obtained a near-complete genome of the primary Fe(II) oxidizer, a species in the family Gallionellaceae, and draft genomes from its flanking community members. A search of the putative extracellular electron transfer pathways in these genomes led to the identification of a homolog of the MtoAB complex [a porin-multiheme cytochrome c system identified in neutrophilic microaerobic Fe(II)-oxidizing Sideroxydans lithotrophicus ES-1] in a Gallionellaceae sp. , and findings of other putative genes involving cytochrome c and multicopper oxidases, such as Cyc2 and OmpB. Genome-enabled metabolic reconstruction revealed that this Gallionellaceae sp. lacks nitric oxide and nitrous oxide reductase genes and may partner with flanking populations capable of complete denitrification to avoid toxic metabolite accumulation, which may explain its resistance to growth in pure culture. This and other revealed interspecies interactions and metabolic interdependencies in nitrogen and carbon metabolisms may allow these organisms to cooperate effectively to achieve robust chemolithoautotrophic NDFO. Overall, the results significantly expand our knowledge of NDFO and suggest a range of genetic targets for further exploration.
Research on Time-Validity and Incremental Association Rules

Association rule mining is an important research field in data mining. Current association-rule methods mainly depend on the support-confidence framework. The strategy is not quite effective in consideration of the time-sensitive factor and correlation problem between antecedent and consequent of rules. To solve this problem, a novel association rules framework has been proposed: time-validity support and time-validity match. First, we define a new match as the substitution of confidence for coping with the correlation problem between antecedence and consequence of rules. Moreover, by embedding the time-entropy factor into the new support-match framework, the time-sensitive can be solved. Finally, an example is given to prove the feasibility and superiority of the new method. On the basis of this, we propose a new incremental algorithm and the idea of performance. Experimental results and comparisons with traditional incremental method demonstrate the effectiveness of the proposed framework.
Information Technology Security Threats to Modern e-Enabled Aircraft: A Cautionary Note

Most passengers, airlines, and the aircraft industry in general are used to very high safety standards and precautions surrounding aircraft systems. As the computerization of aircraft steadily progresses, the question of security (that is, the protection against intentional manipulations) becomes increasingly relevant. This paper focuses on these security challenges. In particular, it adds the following contributions: It assesses the current state of public research on aircraft information technology security and contrasts it with an evaluation of the threat level through a discussion of recent attacks and vulnerabilities. This shows that many attack vectors are not protected against by the state-of-the-art technology implemented in today’s aircraft. In addition, increasing digitalization, connectivity, and similar developments have led to so-called 'e-enabled' aircraft with an ever larger attack surface. This results in challenges to the aircraft industry and lead to a requirement for additional technica.
AR Record&Replay: situated compositing of video content in mobile augmented reality

In this paper we present a novel approach to record and replay video content composited in-situ with a live view of the real environment. Our real-time technique works on mobile phones, and uses a panorama-based tracker to create visually seamless and spatially registered overlay of video content. We apply a temporal foreground-background segmentation of video footage and show how the segmented information can be precisely registered in real-time in the camera view of a mobile phone. We describe the user interface and the video post effects implemented in our prototype as well as our approach with a skateboard training application. Our technique can also be used with online video material and supports the creation of augmented situated documentaries.
A Proof Theory for DL-Lite

In this work we propose an alternative approach to inference in DLLite, based on a reduction to reasoning in an extension of function-free Horn Logic (EHL). We develop a calculus for EHL and prove its soundness and completeness. We also show how to achieve decidability by means of a specific strategy, and how alternative strategies can lead to improved results in specific cases. On the one hand, we propose a strategy that mimics the query-answering technique based on first computing a query rewriting and then evaluating it. On the other hand, we propose strategies that allow one to anticipate the grounding of atoms, and that might lead to better performance in the case where the size of the TBox is not dominated by the size of the data.
Cellular and Network Mechanisms of Spike‐Wave Seizures

Summary: Spike‐wave seizures are often considered a relatively “pure” form of epilepsy, with a uniform defect present in all patients and involvement of the whole brain homogenously. Here, we present evidence against these common misconceptions. Rather than a uniform disorder, spike‐wave rhythms arise from the normal inherent network properties of brain excitatory and inhibitory circuits, where they can be provoked by many different insults in several different brain networks. Here we discuss several different cellular and molecular mechanisms that may contribute to the generation of spike‐wave seizures, particularly in idiopathic generalized epilepsy. In addition, we discuss growing evidence that electrical, neuroimaging, and molecular changes in spike‐wave seizures do not involve the entire brain homogenously. Rather, spike‐wave discharges occur selectively in some thalamocortical networks, while sparing others. It is hoped that improved understanding of the heterogeneous defects and selective brain regions involved will ultimately lead to more effective treatments for spike‐wave seizures.
Induction of AP-1 DNA-binding activity and c-fos mRNA by the adenovirus 243R E1A protein and cyclic AMP requires domains necessary for transformation

The 243R E1A protein can act in synergy with cyclic AMP to induce AP-1 DNA-binding activity and c-fos mRNA in mouse S49 cells. A series of deletion mutants was used to identify two domains of the 243R protein that were required for these effects. Interestingly, these domains correlated precisely with regions known to be necessary for E1A-mediated transformation. One domain was located at the N terminus of E1A. The other domain spanned residues 36 to 81, corresponding to conserved region 1 of E1A. S49 cellular proteins that associate with E1A were coimmunoprecipitated with anti-E1A antibody. These included the previously identified proteins p300, p130, p107, p105Rb, and cyclin A. In addition, proteins of 90 kDa and a series of proteins in the 120- to 170-kDa range were identified. Binding of p300, p90, and the 120- to 170-kDa proteins was abolished in cells expressing mutants of E1A that were unable to induce AP-1 DNA-binding activity and c-fos mRNA. These data strongly suggest that specific cellular E1A-binding proteins are involved in the induction of AP-1 DNA-binding activity and c-fos mRNA by the synergistic action of the 243R E1A protein and cyclic AMP and that these transcriptional events are related to the transformation process.
Adult Lifespan Cognitive Variability in the Cross-Sectional Cam-CAN Cohort

This study examines variability across the age span in cognitive performance in a cross-sectional, population-based, adult lifespan cohort from the Cambridge Centre for Ageing and Neuroscience (Cam-CAN) study (n = 2680). A key question we highlight is whether using measures that are designed to detect age-related cognitive pathology may not be sensitive to, or reflective of, individual variability among younger adults. We present three issues that contribute to the debate for and against age-related increases in variability. Firstly, the need to formally define measures of central tendency and measures of variability. Secondly, in addition to the commonly addressed location-confounding (adjusting for covariates) there may exist changes in measures of variability due to confounder sub-groups. Finally, that increases in spread may be a result of floor or ceiling effects; where the measure is not sensitive enough at all ages. From the Cam-CAN study, a large population-based dataset, we demonstrate the existence of variability-confounding for the immediate episodic memory task; and show that increasing variance with age in our general cognitive measures is driven by a ceiling effect in younger age groups.
"Touch me": workshop on tactile user experience evaluation methods

In this workshop we plan to explore the possibilities and challenges of physical objects and materials for evaluating the User Experience (UX) of interactive systems. These objects should face shortfalls of current UX evaluation methods and allow for a qualitative (or even quantitative), playful and holistic evaluation of UX -- without interfering with the users' personal experiences during interaction. This provides a tactile enhancement to a solely visual stimulation as used in classical evaluation methods. The workshop serves as a basis for networking and community building with interested HCI researchers, designers and practitioners and should encourage further development of the field of tactile UX evaluation.
Some asymptotic results on generalized penalized spline smoothing

Summary. The paper discusses asymptotic properties of penalized spline smoothing if the spline basis increases with the sample size. The proof is provided in a generalized smoothing model allowing for non‐normal responses. The results are extended in two ways. First, assuming the spline coefficients to be a priori normally distributed links the smoothing framework to generalized linear mixed models. We consider the asymptotic rates such that the Laplace approximation is justified and the resulting fits in the mixed model correspond to penalized spline estimates. Secondly, we make use of a fully Bayesian viewpoint by imposing an a priori distribution on all parameters and coefficients. We argue that with the postulated rates at which the spline basis dimension increases with the sample size the posterior distribution of the spline coefficients is approximately normal. The validity of this result is investigated in finite samples by comparing Markov chain Monte Carlo results with their asymptotic approximation in a simulation study.
Cross Time-Frequency Analysis for Combining Information of Several Sources: Application to Estimation of Spontaneous Respiratory Rate from Photoplethysmography

A methodology that combines information from several nonstationary biological signals is presented. This methodology is based on time-frequency coherence, that quantifies the similarity of two signals in the time-frequency domain. A cross time-frequency analysis method, based on quadratic time-frequency distribution, has been used for combining information of several nonstationary biomedical signals. In order to evaluate this methodology, the respiratory rate from the photoplethysmographic (PPG) signal is estimated. The respiration provokes simultaneous changes in the pulse interval, amplitude, and width of the PPG signal. This suggests that the combination of information from these sources will improve the accuracy of the estimation of the respiratory rate. Another target of this paper is to implement an algorithm which provides a robust estimation. Therefore, respiratory rate was estimated only in those intervals where the features extracted from the PPG signals are linearly coupled. In 38 spontaneous breathing subjects, among which 7 were characterized by a respiratory rate lower than 0.15 Hz, this methodology provided accurate estimates, with the median error {0.00; 0.98} mHz ({0.00; 0.31}%) and the interquartile range error {4.88; 6.59} mHz ({1.60; 1.92}%). The estimation error of the presented methodology was largely lower than the estimation error obtained without combining different PPG features related to respiration.
An Efficient Visual Hull Computation Algorithm

In this paper we describe an efficient algorithm for computing the visual hull of an object. This problem is equivalent to computing the intersection of generalized cones. The naive visual hull computation algorithm requires intersecting 3D polyhedra. We exploit the special structure of generalized cone polyhedra and show how to reduce this computation to a set of intersections in 2D. Moreover, we describe how the 2D intersections can be carried out efficiently.
Ecosystem dynamics altered by pathogen-mediated changes following invasion of Banksia woodland and Eucalyptus marginata forest biomes of south-western Australia by Phytophthora cinnamomi

Changes in plant species richness and composition, vegetation structure, ecosystem functioning and soil nutrients following invasion of Banksia woodland and Eucalyptus marginata forest biomes by the introduced soilborne multihost plant pathogen Phytophthora cinnamom were determined using space-for-time substitution of diseased and adjoining healthy areas. In most study areas, canopy closure, basal area and number of plant species were significantly lower in old diseased compared with adjoining healthy areas, with diseased front intermediate between the two. In half of the study areas, percentage ground cover and total plant species cover were significantly lower in old diseased compared with adjoining healthy areas, with diseased front intermediate between the two. Evenness, Shannon-Weiner H and Simpson’s D did not significantly change between disease status for the majority of study areas. For ordination of percentage canopy closure and ground cover there was separation of study areas along a disease status gradient and a weak soil fertility gradient. There was significantly less percentage organic carbon, extractable phosphorus and extractable and total potassium in old diseased areas compared with adjoining healthy areas for one-quarter to a third of the study areas. Total phosphorus changed significantly between disease status, but this was due to higher levels in diseased front compared with the old diseased or adjoining healthy areas. For all study areas there was no significant effect of disease status on percentage total nitrogen and pH. The cover of a majority of plant species did not change significantly between disease status with 16% of the total number of perennial species in healthy areas significantly decreasing and 10% significantly increasing in cover in old diseased compared with adjoining healthy areas. As with significant differences in cover between disease status, change in cover of a majority of plant species was not significantly correlated with canopy closure. Cover of 20% of the total number of perennial species in healthy areas was significantly linearly positively correlated with canopy closure and the cover of 10% of plant species was significantly negatively correlated with canopy closure. These species were herbs and shrubs from a range of families with a mixture of functional properties such as Phytophthoria cinnamomi susceptibility, response to fire, rooting type and mycorrhizal association. The paper concludes with a conceptual analysis of core issues and those that cascade out of core issues involved in pathogen and patch plant community interactions.
X-Ray Peak Broadening and In Vitro Dissolution Studies of Thermally Stabilized Nanocrystalline Carbonated Hydroxyapatite

The present work aims to examine the effect of silicon substitution on thermal and in-vitro dissolution properties of carbonated hydroxyapatite. Hydroxyapatite [Ca10(PO4)6(OH)2, HA], carbonate substituted hydroxyapatite [Ca10(PO4)6-x(CO3)x(OH)2, x=1, 1CHA] and carbonate, silicate co-substituted hydroxyapatite [Ca10(PO4)6-x-y(CO3)x(SiO4)y(OH)2, x=1,y=1, 1C1SiHA] nanoparticles were prepared by microwave synthesis method under identical processing conditions. The XRD results of HA, 1CHA and 1C1SiHA correspond to the standard hexagonal HA (JCPDS 9-432). The crystallite size and lattice strain of the synthesized powder particles were estimated by Williamson-Hall isotropic strain model (W-H ISM) from powder X-ray diffraction data. The dislocation density was calculated by Williamson-Smallman formula. The functional groups present in the as-synthesized powder particles were analyzed by Fourier transform infrared (FT-IR) spectroscopy method. The size and the morphology were examined using a transmission electron microscope (TEM). The in-vitro dissolution behaviour of the synthesized powder particles was studied by ethylenediamine tetra-acetic acid (EDTA) titrimetric method. The W-H ISM results confirm that the prepared powder particles of HA, 1CHA and 1C1SiHA are nanocrystalline with an average crystallite size of 40 nm, 36 nm and 32 nm, respectively. Thus the crystallite size of hydroxyapatite was observed to be decreased gradually with increase in substitutions as indicated by the least size for the 1C1SiHA. In addition, the XRD results of powders annealed at 900 °C for 2 h show the improved thermal stability of 1C1SiHA compared to 1CHA. The TEM results show rod-like shaped morphology for HA, near rod-like with modified edge morphology and increased agglomeration for 1CHA and needle-like shaped morphology for 1C1SiHA powder particles. The in-vitro dissolution study results show a gradual increase in the solubility of HA with carbonate and carbonate-silicate co-substitutions. The calculated microstructural parameters, namely, crystallite size, root mean squared strain and dislocation density were correlated with in-vitro dissolution behaviour of hydroxyapatites.
Release of Vasodilator Prostaglandin, PGI from Isolated Rat Lung during Vasoconstriction

Prostaglandins are generated by the lungs and released into the circulation. Since inhibitors of prostaglandin synthesis enhance hypoxic pulmonary vasoconstriction, we wondered whether vasodilator prostacyclin was synthesized by the lungs in response to vasoconstriction. To test this hypothesis, we measured vasoconstriction induced by angiotensin II in isolated rat lungs before and after inhibition of prostaglandin synthetase. We found that sodium meclofenamate enhanced and prostacyclin and its precursor arachidonate abolished pulmonary vasoconstriction. In lungs labeled with14C-arachidonate, effluent radioactivity increased after angiotensen Il-induced vasoconstriction. Hypoxic vasoconstriction, but not hypoxia per se, caused an increase in lung effluent radioactivity. Chromatographic analysis of lung effluent showed that 6-keto-prostaglandin F, was the major arachidonic acid metabolite released during pulmonary vasoconstriction. We concluded that prostacyclin is produced by the lungs in response to vasoconstriction. Hypoxia per se seems not to be the adequate stimulus for enhanced lung prostacyclin formation. Lung prostacyclin may protect the pulmonary circulation against excessive vasoconstriction. Circ Res 48:207-213, 1981