Miracle-dz/UniFAR-FTUs huggingface dataset:
PI3K is involved in L‐selectin‐ and PSGL‐1‐mediated neutrophil rolling on E‐selectin via F‐actin redistribution and assembly

L‐selectin and P‐selectin glycoprotein ligand‐1 (PSGL‐1) are adhesion molecules that play critical roles in neutrophil rolling during inflammation and lymphocyte homing. On the other hand they also function as signaling receptors to induce cytoskeleton changes. The present study is to investigate the signaling kinases responsible for the F‐actin changes mediated by L‐selectin and PSGL‐1 during neutrophil rolling on E‐selectin. Western blot analysis demonstrated that PI3K activation, peaking within 5 min, was induced by ligation of L‐selectin and PSGL‐1 with E‐selectin, and that Vav1 (the pivotal downstream effector of PI3K signaling pathway involved in cytoskeleton regulation) was recruited to the membrane and tyrosine‐phosphorylated, depending on PI3K. Furthermore, the F‐actin redistribution and assembly mediated by ligation with E‐selectin were blocked by LY294002, a PI3K specific inhibitor. Additional experiments showed that PI3K activity was involved in neutrophil rolling on E‐selectin. However, Syk/Zap70, the well‐known upstream kinase of PI3K, was not involved in this event. These data suggest that PI3K is required for the F‐actin‐based cytoskeleton changes during neutrophil rolling on E‐selectin, which may consequently regulate the rolling event. J. Cell. Biochem. 110: 910–919, 2010. © 2010 Wiley‐Liss, Inc.
Gene therapy for inherited retinal degenerations: initial successes and future challenges

Inherited retinal degenerations are a clinically and genetically heterogeneous group of conditions that have historically shared an untreatable course. In recent years, however, a wide range of therapeutic strategies have demonstrated efficacy in preclinical studies and entered clinical trials with a common goal of improving visual function for patients affected with these conditions. Gene therapy offers a particularly elegant and precise opportunity to target the causative genetic mutations underlying these monogenic diseases. The present review will provide an overview of gene therapy with particular emphasis on key clinical results to date and challenges for the future.
GenTHREADER: an efficient and reliable protein fold recognition method for genomic sequences.

A new protein fold recognition method is described which is both fast and reliable. The method uses a traditional sequence alignment algorithm to generate alignments which are then evaluated by a method derived from threading techniques. As a final step, each threaded model is evaluated by a neural network in order to produce a single measure of confidence in the proposed prediction. The speed of the method, along with its sensitivity and very low false-positive rate makes it ideal for automatically predicting the structure of all the proteins in a translated bacterial genome (proteome). The method has been applied to the genome of Mycoplasma genitalium, and analysis of the results shows that as many as 46 % of the proteins derived from the predicted protein coding regions have a significant relationship to a protein of known structure. In some cases, however, only one domain of the protein can be predicted, giving a total coverage of 30 % when calculated as a fraction of the number of amino acid residues in the whole proteome.
Xylitol Affects the Intestinal Microbiota and Metabolism of Daidzein in Adult Male Mice

This study examined the effects of xylitol on mouse intestinal microbiota and urinary isoflavonoids. Xylitol is classified as a sugar alcohol and used as a food additive. The intestinal microbiota seems to play an important role in isoflavone metabolism. Xylitol feeding appears to affect the gut microbiota. We hypothesized that dietary xylitol changes intestinal microbiota and, therefore, the metabolism of isoflavonoids in mice. Male mice were randomly divided into two groups: those fed a 0.05% daidzein with 5% xylitol diet (XD group) and those fed a 0.05% daidzein-containing control diet (CD group) for 28 days. Plasma total cholesterol concentrations were significantly lower in the XD group than in the CD group (p < 0.05). Urinary amounts of equol were significantly higher in the XD group than in the CD group (p < 0.05). The fecal lipid contents (% dry weight) were significantly greater in the XD group than in the CD group (p < 0.01). The cecal microbiota differed between the two dietary groups. The occupation ratios of Bacteroides were significantly greater in the CD than in the XD group (p < 0.05). This study suggests that xylitol has the potential to affect the metabolism of daidzein by altering the metabolic activity of the intestinal microbiota and/or gut environment. Given that equol affects bone health, dietary xylitol plus isoflavonoids may exert a favorable effect on bone health.
Construction of non-diagonal background error covariance matrices for global chemical data assimilation

Abstract. Chemical data assimilation attempts to optimally use noisy observations along with imperfect model predictions to produce a better estimate of the chemical state of the atmosphere. It is widely accepted that a key ingredient for successful data assimilation is a realistic estimation of the background error distribution. Particularly important is the specification of the background error covariance matrix, which contains information about the magnitude of the background errors and about their correlations. As models evolve toward finer resolutions, the use of diagonal background covariance matrices is increasingly inaccurate, as they captures less of the spatial error correlations. This paper discusses an efficient computational procedure for constructing non-diagonal background error covariance matrices which account for the spatial correlations of errors. The correlation length scales are specified by the user; a correct choice of correlation lengths is important for a good performance of the data assimilation system. The benefits of using the non-diagonal covariance matrices for variational data assimilation with chemical transport models are illustrated.
Considerations on terminal antenna design and analysis

The explosion of modern wireless services has drastically increased the need for efficient electrically small antennas for the handheld terminals. However and opposite to electronic devices, efficiency in antennas is limited by fundamental physical principles. In this paper we present a short summary on the theoretical limitation of the performances of electrically small antennas, and then present some design strategies. We then explain some specific points of the numerical analysis tools suitable for electromagnetic analysis and small antenna design. Some practical design examples illustrate the presented notions.
Psychological profiles in patients with symptomatic reticular forms of oral lichen planus: A prospective cohort study

OBJECTIVES To analyze intra, extra-oral symptoms and psychological profiles in symptomatic patients with reticular (R) forms of oral lichen planus (OLP). MATERIALS AND METHODS Thirty symptomatic R-OLP (sR-OLP) patients were compared with an equal number of non-symptomatic R-OLP (nsR-OLP) patients, burning mouth syndrome (BMS) patients, and healthy subjects (HS). The Numeric Rating Scale (NRS), the Total Pain Rating Index (T-PRI), and the Hamilton Rating Scales for Depression (HAM-D) and Anxiety (HAM-A) were administered. Descriptive statistics, the non-parametric ANOVA procedure by Kruskal-Wallis, the exact Fisher test, and the multiple comparison test by the Mann-Whitney U test were performed. RESULTS The median and IQR of the HAM-D and HAM-A were 16.0 (11.7-24.0) and 17.5 (13.7-27.2) for the BMS, 13.5 (12.0-15.0) and 15.5 (10.7-18.0) for the sR-OLP patients, 2.0 (2.0-3.2) and 2.0 (2.0-4.0) for the nsR-OLP patients, and 3.0 (2.0-4.0) and 3.0 (2.0-4.0) for the HS, respectively. The median and IQR of the NRS and T-PRI were 9.0 (7.7-10.0) and 11.0 (9.0-12.2) for the BMS and 9.0 (7.7-10.0) and 11.5 (7.0-13.0) for the sR-OLP patients, respectively. Comparison analysis between the BMS and sR-OLP patients revealed a non-significant difference between the medians of the psychological profile and pain in the two groups (P-value>.05). CONCLUSIONS The oral complaints are correlated with anxious and depressive symptoms in sR-OLP patients. Mood disorders could modulate the pain perception or that patients could develop two different associated oral diseases, OLP and BMS.
CrowdChess: A System to Investigate Shared Game Control in Live-Streams

Recently, gaming live-streams appeared in which the audience interacts without a streamer. These settings sometimes allow the audience to select from a set of input aggregators to mediate how individual contributions are aggregated. We developed CrowdChess, a system which is optimized for the live-streaming context: multiple viewers play chess together in a single game instance against an AI; they suggest moves and further select one of six aggregators to mediate their contributions. In contrast to existing approaches, CrowdChess allows reasoning about the quality of individual and aggregator contributions, and thus it serves as a test bed for how effectively an audience interacts in such settings. We conducted a study in a live-streaming setup (n=12) and contribute insights on the player perception of audience-driven games and show how aggregators in such a small-scale setting are used, for example, the tendency to use group-based aggregators instead of empowering an individual.
Metformin Prevents Tobacco Carcinogen–Induced Lung Tumorigenesis

Activation of the mammalian target of rapamycin (mTOR) pathway is an important and early event in tobacco carcinogen–induced lung tumorigenesis, and therapies that target mTOR could be effective in the prevention or treatment of lung cancer. The biguanide metformin, which is widely prescribed for the treatment of type II diabetes, might be a good candidate for lung cancer chemoprevention because it activates AMP-activated protein kinase (AMPK), which can inhibit the mTOR pathway. To test this, A/J mice were treated with oral metformin after exposure to the tobacco carcinogen 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK). Metformin reduced lung tumor burden by up to 53% at steady-state plasma concentrations that are achievable in humans. mTOR was inhibited in lung tumors but only modestly. To test whether intraperitoneal administration of metformin might improve mTOR inhibition, we injected mice and assessed biomarkers in liver and lung tissues. Plasma levels of metformin were significantly higher after injection than oral administration. In liver tissue, metformin activated AMPK and inhibited mTOR. In lung tissue, metformin did not activate AMPK but inhibited phosphorylation of insulin-like growth factor-I receptor/insulin receptor (IGF-1R/IR), Akt, extracellular signal–regulated kinase (ERK), and mTOR. This suggested that metformin indirectly inhibited mTOR in lung tissue by decreasing activation of insulin-like growth factor-I receptor/insulin receptor and Akt upstream of mTOR. Based on these data, we repeated the NNK–induced lung tumorigenesis study using intraperitoneal administration of metformin. Metformin decreased tumor burden by 72%, which correlated with decreased cellular proliferation and marked inhibition of mTOR in tumors. These studies show that metformin prevents tobacco carcinogen–induced lung tumorigenesis and support clinical testing of metformin as a chemopreventive agent. Cancer Prev Res; 3(9); 1066–76. ©2010 AACR.
Evaluation of Hardware Requirements for Device Management of Constrained Nodes Based on the LWM2M Standard

Nowadays, resource constrained devices are seen as one of the main components for building the Internet of Things (IoT). Typical constraints of such devices are given by the size of the built-in memory, a non-continuous power supply, and limited computing power. A categorization for such constraints into classes is given in RFC7228. The exponential growth of the number of end devices demand for a centralized, automated, and secure device management to handle the complexity of the upcoming IoT. The emerging open standard Lightweight Machine to Machine (LWM2M) is one of the first approaches to meet the requirements for managing constrained devices. A growing variety of implementations of the LWM2M protocol stack became available in the past years. This paper aims to define useful metrics for measuring device management capabilities on constrained nodes. Two relevant open source implementations are compared by their memory usage. The results show that LWM2M is feasible on Class 2 devices.
Robust Generic and Query-based Summarization

We present a robust summarisation system developed within the GATE architecture that makes use of robust components for semantic tagging and coreference resolution provided by GATE. Our system combines GATE components with well established statistical techniques developed for the purpose of text summarisation research. The system supports "generic" and query-based summarisation addressing the need for user adaptation.
Generating summaries for ontology search

This poster proposes a novel approach for generating summaries for ontology search. Following previous work, we define ontology summarization as the problem of ranking and selecting RDF sentences, for which we examine three aspects. Firstly, to assess the salience of RDF sentences in an ontology, we devise a bipartite graph model for representing the ontology and analyze random walks on this graph. Secondly, to reflect how an ontology is matched with user needs expressed via keyword queries, we incorporate query relevance into the selection of RDF sentences. Finally, to improve the unity of a summary, we optimize its cohesion in terms of the connections between constituent RDF sentences. We have implemented an online prototype system called Falcons Ontology Search.
A Fast and Simple Population Code for Orientation in Primate V1

Orientation tuning has been a classic model for understanding single-neuron computation in the neocortex. However, little is known about how orientation can be read out from the activity of neural populations, in particular in alert animals. Our study is a first step toward that goal. We recorded from up to 20 well isolated single neurons in the primary visual cortex of alert macaques simultaneously and applied a simple, neurally plausible decoder to read out the population code. We focus on two questions: First, what are the time course and the timescale at which orientation can be read out from the population response? Second, how complex does the decoding mechanism in a downstream neuron have to be to reliably discriminate between visual stimuli with different orientations? We show that the neural ensembles in primary visual cortex of awake macaques represent orientation in a way that facilitates a fast and simple readout mechanism: With an average latency of 30–80 ms, the population code can be read out instantaneously with a short integration time of only tens of milliseconds, and neither stimulus contrast nor correlations need to be taken into account to compute the optimal synaptic weight pattern. Our study shows that—similar to the case of single-neuron computation—the representation of orientation in the spike patterns of neural populations can serve as an exemplary case for understanding the computations performed by neural ensembles underlying visual processing during behavior.
Viral Adaptation to Host Immune Responses Occurs in Chronic Hepatitis B Virus (HBV) Infection, and Adaptation Is Greatest in HBV e Antigen-Negative Disease

ABSTRACT Hepatitis B virus (HBV)-specific T-cell responses are important in the natural history of HBV infection. The number of known HBV-specific T-cell epitopes is limited, and it is not clear whether viral evolution occurs in chronic HBV infection. We aimed to identify novel HBV T-cell epitopes by examining the relationship between HBV sequence variation and the human leukocyte antigen (HLA) type in a large prospective clinic-based cohort of Asian patients with chronic HBV infection recruited in Australia and China (n = 119). High-resolution 4-digit HLA class I and II typing and full-length HBV sequencing were undertaken for treatment-naïve individuals (52% with genotype B, 48% with genotype C, 63% HBV e antigen [HBeAg] positive). Statistically significant associations between HLA types and HBV sequence variation were identified (n = 49) at 41 sites in the HBV genome. Using prediction programs, we determined scores for binding between peptides containing these polymorphisms and associated HLA types. Among the regions that could be tested, HLA binding was predicted for 14/18 (78%). We identified several HLA-associated polymorphisms involving likely known anchor residues that resulted in altered predicted binding scores. Some HLA-associated polymorphisms fell within known T-cell epitopes with matching HLA restriction. Enhanced viral adaptation (defined as the presence of the relevant HLA and the escaped amino acid) was independently associated with HBeAg-negative disease (P = 0.003). Thus, HBV appears to be under immune pressure in chronic HBV infection, particularly in HBeAg-negative disease.
Cytochrome c biogenesis System I

Cytochromes c are widespread respiratory proteins characterized by the covalent attachment of heme. The formation of c‐type cytochromes requires, in all but a few exceptional cases, the formation of two thioether bonds between the two cysteine sulfurs in a –CXXCH– motif in the protein and the vinyl groups of heme. The vinyl groups of the heme are not particularly activated and therefore the addition reaction does not physiologically occur spontaneously in cells. There are several diverse post‐translational modification systems for forming these bonds. Here, we describe the complex multiprotein cytochrome c maturation (Ccm) system (in Escherichia coli comprising the proteins CcmABCDEFGH), also called System I, that performs the heme attachment. System I is found in plant mitochondria, archaea and many Gram‐negative bacteria; the systems found in other organisms and organelles are described elsewhere in this minireview series.
Rendering with Spherical Radiance Transport Maps

In this paper, we propose a real‐time method for rendering soft shadows and inter‐reflections of dynamic objects under complex illumination. In previous methods, many efforts were taken to acquire occlusion and reflection informations for dynamic scene on the fly, and the result image cannot be generated in real time. In our approach, these informations for each object are pre‐computed and stored in well‐defined Spherical Radiance Transport Maps (SRTMs). For distant complex illumination such as environment illumination and area light source, we decompose the illumination to several hundred directional lights. In rendering, we search in SRTMs for occlusion info which may cause shadows, and reflection info which may cause inter‐reflections. Finally we produce realistic soft shadows and inter‐reflections efficiently. Our method is related with but different from previous Pre‐computed Radiance Transfer techniques which are only suitable for static scene.
Proc. of the 2017 conference on Big Data from Space

Very High Spatial Resolution (VHSR) large-scale SAR image databases are still an unresolved issue in the Remote Sensing field. In this work, we propose such a dataset and use it to explore patch-based classification in urban and periurban areas, considering 7 distinct semantic classes. In this context, we investigate the accuracy of large CNN classification models and pre-trained networks for SAR imaging systems. Furthermore, we propose a Generative Adversarial Network (GAN) for SAR image generation and test, whether the synthetic data can actually improve classification accuracy.
GPR39-1b, the 5-transmembrane isoform of GPR39 interacts with neurotensin receptor NTSR1 and modifies its function

Abstract G-protein-coupled receptor 39 (GPR39), a member of the ghrelin receptor family, has a full-length isoform GPR39-1a and a truncated isoform GPR39-1b. While GPR39-1a was clarified as a receptor of Zn2+, the characteristic property of GPR39-1b remains unknown. Therefore, in this study, the molecular functions of GPR39-1b were explored in cell culture. In contrast to GPR39-1a, GPR39-1b showed no response to Zn2+ stimulation in calcium mobilization assays, suggesting that GPR39-1b is not a functional receptor of Zn2+. To understand the signaling interaction of GPR39-1b, we investigated the dimerization between the isoforms, and conducted bioluminescence resonance energy transfer (BRET2) assays. The results indicated that GPR39-1b homodimerized, but did not heterodimerize with GPR39-1a. We subsequently attempted to search the heterodimeric counterparts of GPR39-1b. Neurotensin receptor 1 (NTSR1) was also targeted as a GPR39-1b interacting partner because of its highly conserved amino acid sequence and mRNA localization, which was similar to GPR39-1b. BRET2 assays demonstrated that GPR39-1b heterodimerized with NTSR1. To examine the effect of GPR39-1b on NTRS1-mediated cAMP/PKA signaling, we used the cAMP responsive element-luciferase assays and observed that GPR39-1b attenuated neurotensin-induced NTSR1 signaling. Taken together, our results provided a novel regulatory mechanism for GPR39-1b in NTRS1 signaling.
CUNI at MediaEval 2015 Search and Anchoring in Video Archives: Anchoring via Information Retrieval

In the paper we deal with automatic detection of anchoring segments in a collection of TV programmes. The anchoring segments are intended to be further used as a basis for subsequent hyperlinking to another related video segments. The anchoring segments are therefore supposed to be fetching for the users of the collection. Using the hyperlinks, the users can easily navigate through the collection and find more information about the topic of their interest. We present two approaches, one based on metadata, the second one based on frequencies of proper names and numbers contained in the segments. Both approaches proved to be helpful for dierent aspects of anchoring problem: the segments which contain a large number of proper names and numbers are interesting for the users, while the segments most similar to the video description are highly informative.
Initializing neural networks using decision trees

Existing approaches to the inductive learning problem include Symbolic and Connectionist algorithms. While the Symbolic approach is generally found to run signi(cid:12)cantly faster during learning, the Con-nectionist algorithms are often more accurate at classifying novel examples in the presence of noisy data. This paper presents a technique that determines the topology and initial weights of a neural network using a decision tree, thus combining both approaches. Experimental results on benchmark real-world datasets indicate that this technique outperforms the above mentioned approaches both in e(cid:14)ciency and accuracy.