Miracle-dz/UniFAR-FTUs huggingface dataset:
Interleukin-4 Alters Early Phagosome Phenotype by Modulating Class I PI3K Dependent Lipid Remodeling and Protein Recruitment

Phagocytosis is a complex process that involves membranelipid remodeling and the attraction and retention of key effector proteins. Phagosome phenotype depends on the type of receptor engaged and can be influenced by extracellular signals. Interleukin 4 (IL-4) is a cytokine that induces the alternative activation of macrophages (MΦs) upon prolonged exposure, triggering a different cell phenotype that has an altered phagocytic capacity. In contrast, the direct effects of IL-4 during phagocytosis remain unknown. Here, we investigate the impact of short-term IL-4 exposure (1 hour) during phagocytosis of IgG-opsonized yeast particles by MΦs. By time-lapse confocal microscopy of GFP-tagged lipid-sensing probes, we show that IL-4 increases the negative charge of the phagosomal membrane by prolonging the presence of the negatively charged second messenger PI(3,4,5)P3. Biochemical assays reveal an enhanced PI3K/Akt activity upon phagocytosis in the presence of IL-4. Blocking the specific class I PI3K after the onset of phagocytosis completely abrogates the IL-4-induced changes in lipid remodeling and concomitant membrane charge. Finally, we show that IL-4 direct signaling leads to a significantly prolonged retention profile of the signaling molecules Rac1 and Rab5 to the phagosomal membrane in a PI3K-dependent manner. This protracted early phagosome phenotype suggests an altered maturation, which is supported by the delayed phagosome acidification measured in the presence of IL-4. Our findings reveal that molecular differences in IL-4 levels, in the extracellular microenvironment, influence the coordination of lipid remodeling and protein recruitment, which determine phagosome phenotype and, eventually, fate. Endosomal and phagosomal membranes provide topological constraints to signaling molecules. Therefore, changes in the phagosome phenotype modulated by extracellular factors may represent an additional mechanism that regulates the outcome of phagocytosis and could have significant impact on the net biochemical output of a cell.
Seed Carotenoid and Tocochromanol Composition of Wild Fabaceae Species Is Shaped by Phylogeny and Ecological Factors

Carotenoids distribution and function in seeds have been very scarcely studied, notwithstanding their pivotal roles in plants that include photosynthesis and phytohormone synthesis, pigmentation, membrane stabilization and antioxidant activity. Their relationship with tocochromanols, whose critical role in maintaining seed viability has already been evidenced, and with chlorophylls, whose retention in mature seed is thought to have negative effects on storability, remain also unexplored. Here, we aimed at elucidating seed carotenoids relationship with tocochromanols and chlorophylls with regard to phylogenetic and ecological traits and at understanding their changes during germination. The composition and distribution of carotenoids were investigated in seeds of a wide range of wild species across the Fabaceae (the second-most economically important family after the Poaceae). Photosynthetic pigments and tocochromanols were analyzed by HPLC in mature dry seeds of 50 species representative of 5 subfamilies within the Fabaceae (including taxa that represent all continents, biomes and life forms within the family) and at key timepoints during seedling establishment in three species representative of distinct clades. Total-carotenoids content positively correlated with tocopherols in the basal subfamilies Detarioideae, Cercidoideae, and Dialioideae, and with chlorophylls in the Papilionoideae. Papilionoideae lacked tocotrienols and had the highest total-carotenoids, chlorophyll and γ-tocopherol contents. Interestingly, lutein epoxide was present in 72% of the species including several herbs from different subfamilies. Overall, species original from temperate biomes presented higher carotenoids and lower tocochromanols levels than those from tropical biomes. Also shrub species showed higher carotenoids content than herbs and trees. During germination, total content of photosynthetic pigments increased in parallel to changes in relative abundance of carotenoids: zeaxanthin and anteraxanthin decreased and β-carotene augmented. Notably, the highest contents of nutritionally valuable carotenoids were found in Papilionoideae subfamily to which all pulses of socio-economic importance belong. The major differences in carotenoids and tocochromanols composition across the Fabaceae are apparently related to phylogeny in conjunction with ecological traits such as biome and growth form.
Understanding the characteristics of online commenting

In this poster, we investigate the characteristics of online commenting behaviors which can influence on the popularity of various online contents, such as user created contents. To understand the behaviors, we make three dataset, which are crawled from two online discussion forums and one online community. We, first, analyze our dataset in aspects of thread lifetime and the number of comments per thread. Then we cluster and classify threads with two characteristics of the lifetime and the number of comments. Finally we study the characteristic of the number of comments per user.
Large scale cut plane: an occlusion management technique for immersive dense 3D reconstructions

Dense 3D reconstructions of real-world environments become wide spread and are foreseen to act as data base to solve real world problems, such as remote inspections. Therefore not only scene viewing is required but also the ability to interact with the environment, such as selection of a user-defined part of the reconstruction for later usage. However, inter-object occlusion is inherent to large dense 3D reconstructions, due to scene geometry or reconstruction artifacts that might result in object containment. Since prior art lacks approaches for occlusion management in environments that consist of one or multiple (large) continuous surfaces, we propose the novel technique Large Scale Cut Plane that enables segmentation and subsequent selection of visible, partly or fully occluded patches within a large 3D reconstruction, even at far distance. We combine Large Scale Cut Plane with an immersive virtual reality setup to foster 3D scene understanding and natural user interactions. We furthermore present results from a user study where we investigate performance and usability of our proposed technique compared to a baseline technique. Our results indicate Large Scale Cut Plane to be superior in terms of speed and precision, while we found need of improvement of the user interface. The presented investigations has to the authors' best knowledge not been subject to previous research.
Bicaudal Is a Conserved Substrate for Drosophila and Mammalian Caspases and Is Essential for Cell Survival

Members of the caspase family of cysteine proteases coordinate cell death through restricted proteolysis of diverse protein substrates and play a conserved role in apoptosis from nematodes to man. However, while numerous substrates for the mammalian cell death-associated caspases have now been described, few caspase substrates have been identified in other organisms. Here, we have utilized a proteomics-based approach to identify proteins that are cleaved by caspases during apoptosis in Drosophila D-Mel2 cells, a subline of the Schneider S2 cell line. This approach identified multiple novel substrates for the fly caspases and revealed that bicaudal/βNAC is a conserved substrate for Drosophila and mammalian caspases. RNAi-mediated silencing of bicaudal expression in Drosophila D-Mel2 cells resulted in a block to proliferation, followed by spontaneous apoptosis. Similarly, silencing of expression of the mammalian bicaudal homologue, βNAC, in HeLa, HEK293T, MCF-7 and MRC5 cells also resulted in spontaneous apoptosis. These data suggest that bicaudal/βNAC is essential for cell survival and is a conserved target of caspases from flies to man.
PI3K inhibitor enhances the cytotoxic response to etoposide and cisplatin in a newly established neuroendocrine cervical carcinoma cell line

Background Neuroendocrine cervical carcinoma (NECC) is a rare and aggressive subtype of cervical cancer. To date, no NECC cell-based model is available, which hinders the development of new therapeutic strategies for NECC. In this study, we derived a new NECC cell line from an ex vivo biopsy and used it to explore novel drug combination approach for NECC. Results The stable HM-1 cell line displayed high expression levels of the neuroendocrine marker, synaptophysin. HM-1 cell transplantation could induce tumor growth in nude mice. As expected, the combination of etoposide and cisplatin synergistically inhibited HM-1 cell proliferation. Strikingly, when etoposide and cisplatin were combined with PI3K inhibitor BEZ235, the growth of HM-1 cells was significantly reduced. Taken together, the data implied the combination of etoposide and cisplatin with BEZ235 not only inhibited HM-1 cell proliferation but also increased cell apoptosis. Materials and Methods A NECC tissue sample from a 75-year-old female patient was processed to derive a primary cell line annotated as HM-1. The features of HM-1 were analyzed to establish its characteristic profile. Next, HM-1 was treated with PI3K inhibitors, BKM120 and/or BEZ235, in combination with two well-known genotoxic drugs, etoposide and/or cisplatin, to evaluate which combination could serve as a more effective treatment approach. Their inhibiting effects on HM-1 were evaluated by cell viability, apoptosis, and target kinase expression. Conclusions The newly established NECC cell line HM-1 could serve as a cell-based model for NECC research. The synergistic drug combination of PI3K inhibitor with genotoxic drugs might become a potential new treatment strategy against NECC.
Functional decomposition and interactions in hybrid intrusion-tolerant systems

Hybrid wormhole-based architectures have recently been proposed as an approach for building intrusion-tolerant systems. The wormhole, a trusted entity in the system, can be implemented in software using virtualization technology. The architecture of such systems poses the question of distribution of functionality and interactions between three layers: the trusted wormhole, the untrusted part of the replication infrastructure, and the replicated application. For example, a total-ordering service for client requests that is needed for consistent replication can be implemented in the trusted or untrusted part of the infrastructure. In this paper, we discuss this distribution of functionality and the impact on semantics, interfaces, and functional constraints. Finally, we propose a flexible toolkit that eases the implementation and comparison of different architectures.
Application of Thermal Infrared Imagery in Human Action Recognition

Human action recognition has been widely researched and applied in intelligent visual surveillance fields nowadays. Most work on action recognition has been visible-spectrum oriented over the past decade, while the persistence of visual surveillance system increases the demand for night-time action recognition. This paper deals with the problem of night action recognition using thermal infrared imagery. A novel algorithm based on the human action silhouettes energy histograms is proposed. The algorithm first makes use of the statistical background model and background subtraction method to extract the human action silhouettes, while calculating the silhouette energy images for the action sequences. Then, the histograms of oriented gradients are computed from the silhouette energy images. Finally, the human action is represented by the energy histograms features, and recognized by using the Euclidean distance and nearest neighbor classifier. An infrared human action database was built to provide a foundation for night action recognition. Experimental results using the infrared thermal action data show the effective of this method.
Forecasting China’s Annual Biofuel Production Using an Improved Grey Model

Biofuel production in China suffers from many uncertainties due to concerns about the government’s support policy and supply of biofuel raw material. Predicting biofuel production is critical to the development of this energy industry. Depending on the biofuel’s characteristics, we improve the prediction precision of the conventional prediction method by creating a dynamic fuzzy grey–Markov prediction model. Our model divides random time series decomposition into a change trend sequence and a fluctuation sequence. It comprises two improvements. We overcome the problem of considering the status of future time from a static angle in the traditional grey model by using the grey equal dimension new information and equal dimension increasing models to create a dynamic grey prediction model. To resolve the influence of random fluctuation data and weak anti-interference ability in the Markov chain model, we improve the traditional grey–Markov model with classification of states using the fuzzy set theory. Finally, we use real data to test the dynamic fuzzy prediction model. The results prove that the model can effectively improve the accuracy of forecast data and can be applied to predict biofuel production. However, there are still some defects in our model. The modeling approach used here predicts biofuel production levels based upon past production levels dictated by economics, governmental policies, and technological developments but none of which can be forecast accurately based upon past events.
Sugar versus fat: elimination of glycogen storage improves lipid accumulation in Yarrowia lipolytica

&NA; Triacylglycerol (TAG) and glycogen are the two major metabolites for carbon storage in most eukaryotic organisms. We investigated the glycogen metabolism of the oleaginous Yarrowia lipolytica and found that this yeast accumulates up to 16% glycogen in its biomass. Assuming that elimination of glycogen synthesis would result in an improvement of lipid accumulation, we characterized and deleted the single gene coding for glycogen synthase, YlGSY1. The mutant was grown under lipogenic conditions with glucose and glycerol as substrates and we obtained up to 60% improvement in TAG accumulation compared to the wild‐type strain. Additionally, YlGSY1 was deleted in a background that was already engineered for high lipid accumulation. In this obese background, TAG accumulation was also further increased. The highest lipid content of 52% was found after 3 days of cultivation in nitrogen‐limited glycerol medium. Furthermore, we constructed mutants of Y. lipolytica and Saccharomyces cerevisiae that are deleted for both glycogen and TAG synthesis, demonstrating that the ability to store carbon is not essential. Overall, this work showed that glycogen synthesis is a competing pathway for TAG accumulation in oleaginous yeasts and that deletion of the glycogen synthase has beneficial effects on neutral lipid storage. Graphical Abstract Figure. Glycogen and neutral lipid synthesis are competing pathways and the elimination of glycogen storage results in improved lipid synthesis in the yeast Yarrowia lipolytica. Figure. No caption abailable.
Cannabinoid CB1 and Cholecystokinin CCK2 Receptors Modulate, in an Opposing Way, Electrically Evoked [3H]GABA Efflux from Rat Cerebral Cortex Cell Cultures: Possible Relevance for Cortical GABA Transmission and Anxiety

The effects of treatments with cannabinoid (CB)1 and cholecystokinin (CCK)2 receptor agonists and antagonists, as well as compounds that enhance endocannabinoid signaling by inhibiting degradation, e.g., the fatty acid amide hydrolase inhibitor 3′-carbamoyl-biphenyl-3-yl-cyclohexylcarbamate (URB597) or the endocannabinoid reuptake inhibitor (5Z,8Z,11Z,14Z)-N-(3-furanylmethyl)-5,8,11,14-eicosatetraenamide (UCM707), were studied both on spontaneous and electrically evoked [3H]GABA efflux from rat cerebral cortex cell cultures. The CCK2 receptor agonist CCK-8S, the CB1 receptor agonist (R)-(+)-[2,3-dihydro-5-methyl-3-(4-morpholinylmethyl)pyrrolo[1,2,3-de]-1,4-benzoxazin-6-yl]-1-naphthalenylmethanone (WIN55,212-2), URB597, UCM707, the CB1 receptor antagonist N-piperidino-5-(4-chlorophenyl)-1-(2,4-dichlorophenyl)-4-methyl-3-pyrazole-carboxamide (SR141716A), and the CCK2 receptor antagonist 2-[2-(5-Br-1H-indol-3-yl)ethyl]-3-[3-(1-methylethoxy)phenyl]-4-(3H)-quinazolinone (LY225910) did not affect spontaneous [3H]GABA efflux. CCK-8S concentration-dependently increased electrically evoked [3H]GABA overflow, and this effect was prevented by LY225910. WIN55,212-2, URB597, and UCM707 induced a reduction of electrically evoked [3H]GABA overflow. This reduction was counteracted by SR141716A. When CCK-8S and one of cannabinoid-interfering compounds were simultaneously added, at concentrations by themselves ineffective, to the superfusion medium, an enhancement in electrically evoked [3H]GABA efflux was observed. This increase was counteracted by either SR141716A or LY225910 as well as by the inhibitor of protein kinase C, (1R)-2-[12-[(2R)-2-(benzoyloxy)propyl]-3,10-dihydro-4,9-dihydroxy-2,6,7,11-tetramethoxy-3,10-dioxo-1-perylenyl]-1-methylethylcarbonic acid 4-hydroxyphenyl ester (calphostin C). These results indicate that CB1 and CCK2 receptors modulate, in an opposing way, electrically evoked [3H]GABA efflux from rat cerebral cortex cell cultures. The existence of a CB1/CCK2 receptor heteromer on cortical GABA terminals, with a possible relevance for cortical GABA transmission and anxiety, is postulated.
Hepatocyte nuclear factor 1alpha gene inactivation impairs chromatin remodeling and demethylation of the phenylalanine hydroxylase gene

Hepatocyte nuclear factor 1 alpha (HNF1alpha) is a homeoprotein that is expressed in the liver, kidney, pancreas, and digestive tract. Its inactivation in mouse resulted in decreased transcription of known target genes such as albumin and alpha1-antitrypsin. In contrast, the phenylalanine hydroxylase (PAH) gene was totally silent and unresponsive to normal inducers like glucocorticoids and cyclic AMP in the liver. DNase I and micrococcal nuclease digestion of liver nuclei showed that HNF1alpha inactivation had drastic effects on the chromatin structure of the PAH regulatory regions. Three DNase I-hypersensitive sites (HSSI, HSSII, and HSSIII), typical of the actively transcribed PAH gene, were undetectable in liver from HNF1alpha-deficient animals. Both HSSII and HSSIII elements harbor HNF1 sites, but only the latter has detectable enhancer activity in transient-transfection assays. In addition, the PAH promoter in livers of HNF1alpha-deficient animals was methylated. These results suggest that HNF1alpha could activate transcription through two mechanisms. One implies participation in the recruitment of the general transcription machinery to the promoter, and the second involves the remodeling of chromatin structure and demethylation that would allow transcription factors to interact with their cognate cis-acting elements.
Novel approaches to refractory immune thrombocytopenic purpura.

Chronic immune thrombocytopenic purpura (ITP) is an organ-specific autoimmune bleeding disorder in which autoantibodies are directed against the individual's own platelets, resulting in increased Fc-mediated platelet destruction by macrophages in the reticuloendothelial system. Although ITP is primarily mediated by IgG autoantibodies, the production of these autoantibodies is regulated by the influence of T lymphocytes and antigen-presenting cells (APC). There is evidence that enhanced T-helper cell/APC interactions in patients with ITP may play an integral role in IgG antiplatelet autoantibody production. New therapies may improve platelet production, decrease platelet antibody production, and decrease monocyte function and/or B-cell and T-cell activities. Understanding these cellular immune responses in ITP may lead to the development of more specific immunoregulatory therapies for the management of this disease.
Fast Four‐Way Parallel Radix Sorting on GPUs

Efficient sorting is a key requirement for many computer science algorithms. Acceleration of existing techniques as well as developing new sorting approaches is crucial for many real‐time graphics scenarios, database systems, and numerical simulations to name just a few. It is one of the most fundamental operations to organize and filter the ever growing massive amounts of data gathered on a daily basis. While optimal sorting models for serial execution on a single processor exist, efficient parallel sorting remains a challenge. In this paper, we present a hardware‐optimized parallel implementation of the radix sort algorithm that results in a significant speed up over existing sorting implementations. We outperform all known General Processing Unit (GPU) based sorting systems by about a factor of two and eliminate restrictions on the sorting key space. This makes our algorithm not only the fastest, but also the first general GPU sorting solution.
Raj Agrawal WorkFlow Design in Crowdsourcing - Literature Survey

1. A Survey of Crowdsourcing as a means of Collaboration and the Implications of crowdsourcing for interaction design Crowdsourcing has emerged as a new learning and online collaborative paradigm, in which crowds of people can collaborate and complete a specific task. In this paper, we provide a survey of crowdsourcing as a means of collaboration in three different contexts, namely academic, enterprise, and social. The survey also includes a short inventory of how different factors contribute to the development of crowdsourcing. Finally, we develop and outline open questions, insights, as well as a research agenda for enhancing crowdsourcing development in the perspective of HCI. [1]
Novel pharmacological modulators of autophagy: an updated patent review (2012-2015)

ABSTRACT Introduction: Autophagy is a lysosome-dependent degradation pathway that maintains cellular homeostasis in response to a variety of cellular stresses. Accumulating reports based on animal models have indicated the importance of this catabolic program in many human pathophysiological conditions, including diabetes, neurodegenerative diseases, aging, and cancers. Therefore, autophagy has been highlighted as a novel therapeutic target with a wide range of beneficial effects on human diseases. Here, we review the recent advances of our knowledge toward autophagy, as well as the efforts for developing autophagy modulators. Areas covered: The relevant patents (published at 2012–2015) and the research literature claiming the pharmacological modulation of autophagy are reviewed. Also, their molecular mechanisms and potential therapeutic utilities are discussed. Expert opinion: Considering the molecular machinery involved in autophagy induction, the targeting of autophagy-specific protein is very important to design the therapeutic interventions for specifically treating a variety of autophagy-associated disorders. Many patents and the research literature described in this review have shown promising applications of the relevant autophagy modulators for cancer or neurodegeneration treatments, a few of which are already being considered for clinical evaluation. However, most patents have claimed the modulators of autophagy with little information regarding their mechanisms of action. To design highly potent therapeutics, further work, such as developing compounds that specifically target the autophagy-specific machinery, are required.
USING GAMES TO COLLECT SEMANTIC ANNOTATIONS OF MUSIC

TO BE WRITTEN LAST: (1) Develop human computation games that collect semantic labels (i.e., semantically relevant words) for music. (2) This technique used to collect semantic information about images. (3) Describe Listen Game as a multiplayer, online game with realtime feedback. (4) Produces high-quality semantic labels for music. (5) Using this data, we train a supervised multiclass labeling (SML) model and show that this model can annotate and retrieve music. The abstract should be placed at the top left column and should contain about 150-200 words.