Lifelong learning in evolving graphs with limited labeled data and unseen class detection

Large-scale graph data in the real-world are often dynamic rather than static. The data are changing with new nodes, edges, and even classes appearing over time, such as in citation networks and research-and-development collaboration networks. Graph neural networks (GNNs) have emerged as the standard method for numerous tasks on graph-structured data. In this work, we employ a two-step procedure to explore how GNNs can be incrementally adapted to new unseen graph data. First, we analyze the verge between transductive and inductive learning on standard benchmark datasets. After inductive pretraining, we add unlabeled data to the graph and show that the models are stable. Then, we explore the case of continually adding more and more labeled data, while considering cases, where not all past instances are annotated with class labels. Furthermore, we introduce new classes while the graph evolves and explore methods that automatically detect instances from previously unseen classes. In order to deal with evolving graphs in a principled way, we propose a lifelong learning framework for graph data along with an evaluation protocol. In this framework, we evaluate representative GNN architectures. We observe that implicit knowledge within model parameters becomes more important when explicit knowledge, i.e., data from past tasks, is limited. We find that in open-world node classification, the data from surprisingly few past tasks are sufficient to reach the performance reached by remembering data from all past tasks. In the challenging task of unseen class detection, we find that using a weighted cross-entropy loss is important for stabilit

An Artificially Lattice Mismatched Graphene/Metal Interface: Graphene/Ni/Ir(111)

We report the structural and electronic properties of an artificial graphene/Ni(111) system obtained by the intercalation of a monoatomic layer of Ni in graphene/Ir(111). Upon intercalation, Ni grows epitaxially on Ir(111), resulting in a lattice mismatched graphene/Ni system. By performing Scanning Tunneling Microscopy (STM) measurements and Density Functional Theory (DFT) calculations, we show that the intercalated Ni layer leads to a pronounced buckling of the graphene film. At the same time an enhanced interaction is measured by Angle-Resolved Photo-Emission Spectroscopy (ARPES), showing a clear transition from a nearly-undisturbed to a strongly-hybridized graphene $\pi$-band. A comparison of the intercalation-like graphene system with flat graphene on bulk Ni(111), and mildly corrugated graphene on Ir(111), allows to disentangle the two key properties which lead to the observed increased interaction, namely lattice matching and electronic interaction. Although the latter determines the strength of the hybridization, we find an important influence of the local carbon configuration resulting from the lattice mismatch.Comment: 9 pages, 3 figures, Accepted for publication in Phys. Rev.

Morphological evolution of electrochemically plated stripped lithium microstructures by synchrotron X ray phase contrast tomography

Due to its low redox potential and high theoretical specific capacity, Li metal has drawn worldwide research attention because of its potential use in next generation battery technologies such as Li S and Li O2. Unfortunately, uncontrollable growth of Li microstructures LmSs, e.g., dendrites, fibers during electrochemical Li stripping plating has prevented their practical commercialization. Despite various strategies proposed to mitigate LmS nucleation and or block its growth, a fundamental understanding of the underlying evolution mechanisms remains elusive. Herein, synchrotron in line phase contrast X ray tomography was employed to investigate the morphological evolution of electrochemically deposited dissolved LmSs nondestructively. We present a 3D characterization of electrochemically stripped Li electrodes with regard to electrochemically plated LmSs. We clarify fundamentally the origin of the porous lithium interface growing into Li electrodes. Moreover, cleavage of the separator caused by growing LmS was experimentally observed and visualized in 3D. Our systematic investigation provides fundamental insights into LmS evolution and enables us to understand the evolution mechanisms in Li electrodes more profoundl

ATF4 links ER stress with reticulophagy in glioblastoma cells

Selective degradation of the endoplasmic reticulum (ER; reticulophagy) is a type of autophagy involved in the removal of ER fragments. So far, amino acid starvation as well as ER stress have been described as inducers of reticulophagy, which in turn restores cellular energy levels and ER homeostasis. Here, we explored the autophagy-inducing mechanisms that underlie the autophagic cell death (ACD)-triggering compound loperamide (LOP) in glioblastoma cells. Interestingly, LOP triggers upregulation of the transcription factor ATF4, which is accompanied by the induction of additional ER stress markers. Notably, knockout of ATF4 significantly attenuated LOP-induced autophagy and ACD. Functionally, LOP also specifically induces the engulfment of large ER fragments within autophagosomes and lysosomes as determined by electron and fluorescence microscopy. LOP-induced reticulophagy and cell death are predominantly mediated through the reticulophagy receptor RETREG1/FAM134B and, to a lesser extent, TEX264, confirming that reticulophagy receptors can promote ACD. Strikingly, apart from triggering LOP-induced autophagy and ACD, ATF4 is also required for LOP-induced reticulophagy. These observations highlight a key role for ATF4, RETREG1 and TEX264 in response to LOP-induced ER stress, reticulophagy and ACD, and establish a novel mechanistic link between ER stress and reticulophagy, with possible implications for additional models of drug-induced ER stress

Frequency domain analysis for detecting pipeline leaks

The original publication can be found at http://scitation.aip.org/hyoThis paper introduces leak detection methods that involve the injection of a fluid transient into the pipeline, with the resultant transient trace analyzed in the frequency domain. Two methods of leak detection using the frequency response of the pipeline are proposed. The inverse resonance method involves matching the modeled frequency responses to those observed to determine the leak parameters. The peak-sequencing method determines the region in which the leak is located by comparing the relative sizes between peaks in the frequency response diagram. It was found that a unique pattern was induced on the peaks of the frequency response for each specific location of the leak within the pipeline. The leak location can be determined by matching the observed pattern to patterns generated numerically within a lookup table. The procedure for extracting the linear frequency response diagram, including the optimum measurement position, the effect of unsteady friction, and the way in which the technique can be extended into pipeline networks, are also discussed within the paper.Pedro J. Lee, John P. Vítkovský, Martin F. Lambert, Angus R. Simpson and James A. Ligget

Timed inhibition of CDC7 increases CRISPR-Cas9 mediated templated repair.

Repair of double strand DNA breaks (DSBs) can result in gene disruption or gene modification via homology directed repair (HDR) from donor DNA. Altering cellular responses to DSBs may rebalance editing outcomes towards HDR and away from other repair outcomes. Here, we utilize a pooled CRISPR screen to define host cell involvement in HDR between a Cas9 DSB and a plasmid double stranded donor DNA (dsDonor). We find that the Fanconi Anemia (FA) pathway is required for dsDonor HDR and that other genes act to repress HDR. Small molecule inhibition of one of these repressors, CDC7, by XL413 and other inhibitors increases the efficiency of HDR by up to 3.5 fold in many contexts, including primary T cells. XL413 stimulates HDR during a reversible slowing of S-phase that is unexplored for Cas9-induced HDR. We anticipate that XL413 and other such rationally developed inhibitors will be useful tools for gene modification

Advances in MASELTOV – Serious Games in a Mobile Ecology of Services for Social Inclusion and Empowerment of Recent Immigrants

Immigration imposes a range of challenges with the risk of social exclusion from the information society (Halfman 1998), such as, getting into communication with the local society and understanding the culture of their host nation. Failure to address these challenges can lead to difficulties in the frame of integrating into the society of the host country, leading to fragmented communities and a range of social issues. As part of a comprehensive suite of services for immigrants, the European project seeks to provide both practical tools and learning services via mobile devices, providing a readily usable resource for immigrants. We introduce recent results, such as the game-based learning aspect of the MASELTOV project is introduced, with the rationale behind its design presented. In doing so, the benefits and implications of mobile platforms and emergent data capture techniques for game-based learning are discussed, as are methods for putting engaging gameplay at the forefront of the experience whilst relying on rich data capture and analysis to provide an effective learning solution

Loperamide, pimozide, and STF-62247 trigger autophagy-dependent cell death in glioblastoma cells

Autophagy is a well-described degradation mechanism that promotes cell survival upon nutrient starvation and other forms of cellular stresses. In addition, there is growing evidence showing that autophagy can exert a lethal function via autophagic cell death (ACD). As ACD has been implicated in apoptosis-resistant glioblastoma (GBM), there is a high medical need for identifying novel ACD-inducing drugs. Therefore, we screened a library containing 70 autophagy-inducing compounds to induce ATG5-dependent cell death in human MZ-54 GBM cells. Here, we identified three compounds, i.e. loperamide, pimozide, and STF-62247 that significantly induce cell death in several GBM cell lines compared to CRISPR/Cas9-generated ATG5- or ATG7-deficient cells, pointing to a death-promoting role of autophagy. Further cell death analyses conducted using pharmacological inhibitors revealed that apoptosis, ferroptosis, and necroptosis only play minor roles in loperamide-, pimozide- or STF-62247-induced cell death. Intriguingly, these three compounds induce massive lipidation of the autophagy marker protein LC3B as well as the formation of LC3B puncta, which are characteristic of autophagy. Furthermore, loperamide, pimozide, and STF-62247 enhance the autophagic flux in parental MZ-54 cells, but not in ATG5 or ATG7 knockout (KO) MZ-54 cells. In addition, loperamide- and pimozide-treated cells display a massive formation of autophagosomes and autolysosomes at the ultrastructural level. Finally, stimulation of autophagy by all three compounds is accompanied by dephosphorylation of mammalian target of rapamycin complex 1 (mTORC1), a well-known negative regulator of autophagy. In summary, our results indicate that loperamide, pimozide, and STF-62247 induce ATG5- and ATG7-dependent cell death in GBM cells, which is preceded by a massive induction of autophagy. These findings emphasize the lethal function and potential clinical relevance of hyperactivated autophagy in GBM

High glucose inhibits human epidermal keratinocyte proliferation for cellular studies on diabetes mellitus

In order to more clarify the delayed wound healing in diabetes mellitus, we cultured the human epidermal keratinocytes in both 6 mM (control group) and 12 mM glucose (high-glucose group) of ‘complete’ MCDB 153 medium. Hyperglycaemia slowed the rate of their proliferation and inhibited their DNA synthesis and the production of total proteins. By 1 month after primary seeding in high-glucose group, the cells ceased their proliferation, whereas the cells in control group grew for more than 40 days. Mean population doublings in high-glucose group was 5·27 (vs. 7·25 in control, P = 0·001), and mean population doubling time during 1 month in high glucose group was 5·43 days (vs. 3·65 days in control, P = 0·02). They indicate that prolonged exposure to high glucose decreases the replicative life span of human epidermal keratinocytes in vitro. Furthermore, analysis of fatty acid contents in membrane phospholipids with thin-layer and gas chromatography showed no difference between the cultured keratinocytes in both conditions. Immunocytochemical staining of glucose transporter 1 shows that 28·1% of cells in high-glucose group were almost twice positive of those in control group (13·2%, P = 0·008). The mechanism of the ill effects of high glucose on epidermal keratinocytes is not so far clear, but it indicates the possibility of any direct effect of hyperglycaemia on glucose metabolism without changing lipid metabolism on cell membrane. The high-glucose group presented in this report can be available as an in vitro valuable study model of skin epidermal condition on diabetes mellitus.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/72307/1/j.1742-4801.2005.00148.x.pd