cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
A microparticle platform for STING-targeted immunotherapy enhances natural killer cell- and CD8 + T cell-mediated anti-tumor immunity
Creators: name: Junkins, R.D.
name: Bachelder, E.M.
name: Ting, J.P.Y.
name: Tiet, P.
name: Gallovic, M.D.
name: Watkins-Schulz, R.
name: Batty, C.
name: Ainslie, K.M.
Publisher: name: Elsevier Ltd
Year: 2019

description: Immunotherapies have significantly improved cancer patient survival, but response rates are still limited. Thus, novel formulations are needed to expand the breadth of immunotherapies. Pathogen associated molecular patterns (PAMPs) can be used to stimulate an immune response, but several pathogen recognition receptors are located within the cell, making delivery challenging. We have employed the biodegradable polymer acetalated dextran (Ace-DEX) to formulate PAMP microparticles (MPs) in order to enhance intracellular delivery. While treatment with four different PAMP MPs resulted in tumor growth inhibition, cyclic GMP-AMP (cGAMP) MPs were most effective. cGAMP MPs showed anti-tumor efficacy at doses 100-1000 fold lower than published doses of soluble cGAMP in two murine tumor models. Treatment with cGAMP MPs resulted in increased natural killer cell numbers in the tumor environment. Immune cell depletion studies confirmed that NK cells were responsible for the anti-tumor efficacy in an aggressive mouse melanoma model. NK cells and CD8 + T cells were both required for early anti-tumor function in a triple negative breast cancer model. In summary, cGAMP MP treatment results in NK and T cell-dependent anti-tumor immune response.
Universal spin-1/2 fermion field localization on a 5D braneworld
Creators: name: Barbosa-Cendejas, Nandinii
name: Malagón-Morejón, Dagoberto
name: Mora-Luna, Refugio Rigel
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences
subject: 00A79

description: In this letter we have proposed a natural way of determine the Yukawa coupling $F(z)\barΨΨ$ for the 5D bulk action, the form of the $F(z)$ function allows us to localize the spin--$\frac{1}{2}$ fermionic fields in the paradigm of the 5D braneworld scenarios. The structure acquired by the $V_{L,R}$ potentials is induced by the ansatz for the $F(z)$ function and we show that this choice allows the localization of the left-- or right--chiral KK zero modes $L_{0}(z)$, $R_{0}(z)$ and excludes the tachyonic modes of the KK mass spectrum $m_{L_{n}}$ and $m_{R_{n}}$. The proposal for the function $F(z)$ leaves behind other speculative proposals since it is independent of the braneworld model, hence the form for the Yukawa coupling here presented is the most natural choice. This is shown most evidently if we set $M=\pm 3/2$, which is a more phenomenologically viable ansatz. This choice allows for a direct relation between the localization of the ground state for the left-- or right--chiral KK mass spectrum and the localization of the zero mode for the 4D graviton in the brane. As a bonus, we include a brief discussion about the existence of a left-- or right--chiral KK zero mode decoupled from the corresponding continuous KK mass spectrum, as well as the possible existence of a mass gap, due to the asymptotic nature of the potentials $V_{R,L}$.
description: 7 pages in General Relativity and Gravitation, Volume 47, Issue , 2015
Lepton Asymmetric Universe
Creators: name: Kawasaki, Masahiro
name: Murai, Kai
Publisher: name: arXiv
Year: 2022
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: The recent observation of $^4$He implies that our universe has a large lepton asymmetry. We consider the Affleck-Dine (AD) mechanism for lepton number generation. In the AD mechanism, non-topological solitons called L-balls are produced, and the generated lepton number is confined in them. The L-balls protect the generated lepton number from being converted to baryon number through the sphaleron processes. We study the formation and evolution of the L-balls and find that the universe with large lepton asymmetry suggested by the recent $^4$He measurement can be realized.
description: 12 pages, 1 figure
Danger-associated extracellular ATP counters MDSC therapeutic efficacy in acute GVHD
Creators: name: Hill, G.R.
name: Blazar, B.R.
name: Munn, D.H.
name: Hippen, K.
name: Ting, J.P.-Y.
name: Serody, J.S.
name: Zeiser, R.
name: Loschi, M.
name: Murray, P.J.
name: Bronte, V.
name: Miller, J.S.
name: Dysthe, J.
name: Krepps, W.
name: Ma, L.
name: Farady, C.J.
name: McDonald-Hyman, C.
name: Panthera, J.
name: Jameson, S.C.
name: Iwawaki, T.
name: Koehn, B.H.
name: Thangavelu, G.
name: Zaiken, M.
name: Saha, A.
name: Cooper, M.A.
name: Murphy, W.J.
Publisher: name: American Society of Hematology
Year: 2019

description: Myeloid-derived suppressor cells (MDSCs) can subdue inflammation. In mice with acute graft-versus-host disease (GVHD), donor MDSC infusion enhances survival that is only partial and transient because of MDSC inflammasome activation early posttransfer, resulting in differentiation and loss of suppressor function. Here we demonstrate that conditioning regimen-induced adenosine triphosphate (ATP) release is a primary driver of MDSC dysfunction through ATP receptor (P2x7R) engagement and NLR pyrin family domain 3 (NLRP3) inflammasome activation. P2x7R or NLRP3 knockout (KO) donor MDSCs provided significantly higher survival than wild-type (WT) MDSCs. Although in vivo pharmacologic targeting of NLRP3 or P2x7R promoted recipient survival, indicating in vivo biologic effects, no synergistic survival advantage was seen when combined with MDSCs. Because activated inflammasomes release mature interleukin-1β (IL-1β), we expected that IL-1β KO donor MDSCs would be superior in subverting GVHD, but such MDSCs proved inferior relative to WT. IL-1β release and IL-1 receptor expression was required for optimal MDSC function, and exogenous IL-1β added to suppression assays that included MDSCs increased suppressor potency. These data indicate that prolonged systemic NLRP3 inflammasome inhibition and decreased IL-1β could diminish survival in GVHD. However, loss of inflammasome activation and IL-1β release restricted to MDSCs rather than systemic inhibition allowed non-MDSC IL-1β signaling, improving survival. Extracellular ATP catalysis with peritransplant apyrase administered into the peritoneum, the ATP release site, synergized with WT MDSCs, as did regulatory T-cell infusion, which we showed reduced but did not eliminate MDSC inflammasome activation, as assessed with a novel inflammasome reporter strain. These findings will inform future clinical using MDSCs to decrease alloresponses in inflammatory environments.
Surface Fermi arcs in $Z_2$ Weyl semimetals $A_3 Bi$ (A=Na, K, Rb)
Creators: name: Gorbar, E. V.
name: Miransky, V. A.
name: Shovkovy, I. A.
name: Sukhachov, P. O.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: The surface Fermi arc states in $Z_2$ Weyl semimetals $A_3 Bi$ (A=Na, K, Rb) are studied by employing a continuum low-energy effective model. It is shown that the surface Fermi arc states can be classified with respect to the ud-parity symmetry. Because of the symmetry, the arcs come in mirror symmetric pairs. The effects of symmetry breaking terms on the structure of the Fermi arcs are also studied. Among other results, we find at least two qualitatively different types of the surface Fermi arcs. The arcs of the first type link disconnected sheets of the bulk Fermi surface, while arcs of the second type link different points of the same bulk Fermi surface sheet.
description: 17 pages, 4 multi-panel figures; v2: published version with minor corrections, new references and a slightly reorganized text
Modeling human motion using manifold learning and factorized generative models
Creators: name: Lee, Chan-Su
Publisher: name: No Publisher Supplied
Year: 2007

description: Modeling the dynamic shape and appearance of articulated moving objects is essential for human motion analysis, tracking, synthesis, and other computer vision problems. Modeling the shape and appearance of human motion is challenging due to the high dimensionality of the articulated human motion, variations of shape and appearance from different views and in different people, and the nonlinearity in shape and appearance deformations in the observed sequences. Recent interest in modeling human motion is originated from the various potential real-world applications such as visual surveillance, human-computer interaction, video analysis, computer animation, etc.We present a novel framework to model dynamic shape and appearance using nonlinear manifold embedding and factorization. We investigate different representations to embed high-dimensional human motion sequences in low dimensional spaces by supervised and unsupervised manifold learning techniques to achieve representations that capture the intrinsic structure of the motion. Nonlinear dimensionality reduction techniques based on visual data and kinematic data are applied to discover low dimensional intrinsic manifold representation for body configuration. Also, we investigate the use of supervised manifold learning from a known manifold topology to model deformation of manifolds from an ideal case. By learning nonlinear mapping from the embedding space to the input shape or appearance, we can generate shape and appearance sequences according to the motion state on the embedded manifold.We present a decomposable generative model to analyze shape and appearance variations by different factors such as person's style, motion type, and view point. We use multilinear analysis in the nonlinear mapping coefficient space to factorize shape and appearance variations. Also, we investigate learning generative models to represent continuous body configuration and continuous view manifolds in a product space (i.e. body configuration manifold x view manifold). The proposed factorized generative models provide rich models for the analysis of dynamic shape and appearance of human motion. We applied the model in computer vision problems such as inferring 3D body pose from 2D images, tracking human motion with continuous view variations within the Bayesian framework, and gait recognition. We also applied our model for facial expression analysis, tracking, recognition and synthesis.
Searching for Candidates of Orbital Decays among Transit Exoplanets
Creators: name: Yeh, Li-Chin
name: Jiang, Ing-Guey
name: A-thano, Napaporn
Publisher: name: arXiv
Year: 2023
Subjects: subject: Earth and Planetary Astrophysics (astro-ph.EP)
subject: FOS: Physical sciences

description: Transit observations have become an important technique to probe exoplanets. Therefore, there are many projects carrying on organized observations of transit events, which make a huge amount of light-curve and transit timing data available. We consider this as an excellent opportunity to search for possible orbital decays of exoplanets from this big number of mid-transit times through data-model fitting with both fixed-orbit and orbit-decay models. In order to perform this task, we collect mid-transit-time data from several sources and construct the most complete database up to date. Among 144 hot Jupiters in our study, HAT-P-51b, HAT-P-53b, TrES-5b, WASP-12b are classified as the orbit-decay cases. Thus, in addition to reconfirming WASP-12b as an orbit-decay planet, our results indicate that HAT-P-51b, HAT-P-53b, TrES-5b are potential orbit-decay candidates.
description: 12 pages, 5 figures, 5 tables, accepted by New Astronomy
Electrical transport properties of atomically thin WSe2 using perpendicular magnetic anisotropy metal contacts
Creators: name: Gupta, S.
name: Ohshima, R.
name: Ando, Y.
name: Endo, T.
name: Miyata, Y.
name: Shiraishi, M.
Publisher: name: arXiv
Year: 2023
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: Tungsten diselenide, WSe2 shows excellent properties and become very promising material among two dimensional semiconductors. Wide band gap and large spin-orbit coupling along with naturally lacking inversion symmetry in the monolayer WSe2 make it efficient material for spintronics, optoelectronics and valleytronics applications. In this work, we report electrical transport properties of monolayer WSe2 based field effect transistor with most needed multilayer Co/Pt ferromagnetic electrodes exhibiting perpendicular magnetic anisotropy. We studied contacts behaviour by performing I-V curve measurements and estimating Schottky barrier heights (SBHs). SBHs estimated from experimental data are found to be comparatively small, without using any tunnel barrier. This work expands the current understanding of WSe2 based devices and gives insight into the electrical behaviour of Co/Pt metal contacts, which can open great possibilities for spintronic/valleytronic applications.
description: 8 pages, 4 figures
Understanding soil moisture dynamics using observations and climate models
Creators: name: Li, Haibin
Publisher: name: No Publisher Supplied
Year: 2007

description: With the objective to improve our understanding of soil moisture and its long term changes, I analyzed and compared climate model simulations with in situ soil moisture observations. Three studies were conducted to investigate soil moisture variations on seasonal to interannual scales and its long term changes.To investigate soil moisture evolutions on seasonal to interannual scales and the capacity of reanalysis systems to capture the observed characteristics, I analyzed newly updated 19 yr of Chinese soil moisture data and evaluated ERA40, NCEP/NCAR reanalysis (R-1), and NCEP/DOE reanalysis 2 (R-2). Over this region, soil moisture seasonality is in general not strong. Seasonal cycles and interannual variations exhibit considerably spatial diversity. R-2 generally exhibits improved interannual variability and better seasonal patterns of soil moisture than R-1 as a result of incorporating observed precipitation. ERA40 produces a better mean value of soil moisture for most Chinese stations and good interannual variability. In terms of temporal scale - an indicator of anomaly persistence, R-2 has a memory about twice that of the observations for the growing season. The unrealistic long temporal scale of R-2 can be attributed to the deep layer of the land surface model, which is too thick and dominates the soil moisture variability. The analysis highlights the importance of correct soil parameters to land surface processes and points out possible directions in which the reanalysis can be continuously improved to provide more realistic soil moisture outputs.Observations from Ukraine and Russia show significant increases in summer for the period from 1958-1999 that seem contradictory to the classic summer drying issue from early modeling studies. To see whether the latest climate models can capture the observed patterns, I calculated trends in soil moisture simulations from Intergovernmental Panel on Climate Change Fourth Assessment climate models. The upward trends in observations, which cannot be explained by precipitation and temperature changes alone, were found to be much larger than most trends in model realizations. Solar dimming is proposed to have played an important role in modulating soil moisture variations for these two regions.Further, a series off-line sensitivity experiments with a sophisticated land surface model were conducted to investigate possible contribution from solar dimming and elevated CO2 to the observed soil moisture trends for Ukraine and Russia. I demonstrate, by imposing a downward trend to shortwave radiation forcing to mimic the dimming, the observed soil moisture pattern can be essentially reproduced. On the other hand, the effects of elevated CO2 are relatively small for the study period. The results support the hypothesis that solar dimming may have played an important role in regional soil moisture changes.
Algorithmic developments and complexity results for finding maximum and exact independent sets in graphs
Creators: name: Milanic, Martin
Publisher: name: No Publisher Supplied
Year: 2007

description: We consider the maximum independent set and maximum weight independent set problems in graphs. As these problems are generally NP-hard, we study their complexity in hereditary graph classes, that is, in graph classes defined by a set F of forbidden induced subgraphs.We describe a condition on the set F, which guarantees that the maximum independent set problem remains NP-hard in the class of F-free graphs. The same hardness result remains valid even under the additional restriction that the graphs are planar and of maximum degree at most three.We exhibit several cases where the condition is violated, and the problem admits a polynomial-time solution. More specifically, we present polynomial-time algorithms for the maximum independent set problem in:-two graph classes that properly contain claw-free graphs (thus generalizing the classical result for claw-free graphs); -various subclasses of planar and more general graphs;-weighted graphs in certain subclasses of graphs of bounded vertex degree. Our algorithms are based on various approaches. In particular, we develop an extension of the method of finding augmenting graphs. We also make extensive use of some other well-known graph decompositions.We also introduce and study the exact version of the problem, where, instead of finding an independent set of maximum weight, the goal is to find an independent set of given weight. Determining the computational complexity of this problem for line graphs, or for line graphs of bipartite graphs would resolve long standing open problems. Here, we show that:-The exact weighted independent set problem is strongly NP-complete for cubic bipartite graphs.-The problem is solvable in pseudo polynomial time for any of the following graph classes:mK2-free graphs, interval graphs and their generalizations k-thin graphs, circle graphs, chordal graphs, AT-free graphs, (claw, net)-free graphs, distance-hereditary graphs, and graphs of bounded tree- or clique-width.Finally, we show how modular decomposition can be applied to the exact weighted independent set problem. As a corollary, we obtain pseudo-polynomial solutions for the problem in certain subclasses of P5-free and fork-free graphs.
Accurate electronic properties and intercalation voltages of olivine-type Li-ion cathode materials from extended Hubbard functionals
Creators: name: Timrov, Iurii
name: Aquilante, Francesco
name: Cococcioni, Matteo
name: Marzari, Nicola
Publisher: name: arXiv
Year: 2022
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: The design of novel cathode materials for Li-ion batteries would greatly benefit from accurate first-principles predictions of structural, electronic, and magnetic properties as well as intercalation voltages in compounds containing transition-metal elements. For such systems, density-functional theory (DFT) with standard (semi-)local exchange-correlation functionals is of limited use as it often fails due to strong self-interaction errors that are especially relevant in the partially filled $d$ shells. Here, we perform a detailed comparative study of the phospho-olivine cathode materials Li$_x$MnPO$_4$, Li$_x$FePO$_4$, and the mixed transition metal Li$_x$Mn$_{1/2}$Fe$_{1/2}$PO$_4$ ($x=0, 1/4, 1/2, 3/4, 1$) using four electronic-structure methods: DFT, DFT+$U$, DFT+$U$+$V$, and HSE06. We show that DFT+$U$+$V$, with onsite $U$ and intersite $V$ Hubbard parameters determined from first principles and self-consistently with respect to the structural parameters by means of density-functional perturbation theory (linear response), provides the most accurate description of the electronic structure of these challenging compounds. In particular, we demonstrate that DFT+$U$+$V$ displays very clearly "digital" changes in oxidation states of the transition-metal ions in all compounds, including the mixed-valence phases occurring at intermediate Li concentrations, leading to voltages in remarkable agreement with experiments. We show that the inclusion of intersite Hubbard interactions is essential for the accurate prediction of thermodynamic quantities, balancing the drive for localization induced by the onsite $U$ with intersite $V$ orbital hybridizations.
NLRP12 Regulates Anti-viral RIG-I Activation via Interaction with TRIM25
Creators: name: Tseng, W.-T.
name: Guo, H.
name: Jung, J.U.
name: Kang, H.-R.
name: Tam, J.W.
name: Brickey, W.J.
name: Chen, L.
name: Li, F.-J.
name: Chao, C.-W.
name: Tsao, Y.-P.
name: Dzhagalov, I.
name: Lin, D.S.-C.
name: Song, M.-J.
name: Chen, S.-Y.
name: Chen, S.-T.
name: Ting, J.P.-Y.
Publisher: name: Cell Press
Year: 2019

description: Establishing the balance between positive and negative innate immune mechanisms is crucial for maintaining homeostasis. Here we uncover the regulatory crosstalk between two previously unlinked innate immune receptor families: RIG-I, an anti-viral cytosolic receptor activated type I interferon production, and NLR (nucleotide-binding domain, leucine repeat domain-containing protein). We show that NLRP12 dampens RIG-I-mediated immune signaling against RNA viruses by controlling RIG-I's association with its adaptor MAVS. The nucleotide-binding domain of NLRP12 interacts with the ubiquitin ligase TRIM25 to prevent TRIM25-mediated, Lys63-linked ubiquitination and activation of RIG-I. NLRP12 also enhances RNF125-mediated, Lys48-linked degradative ubiquitination of RIG-I. Vesicular stomatitis virus (VSV) infection downregulates NLRP12 expression to allow RIG-I activation. Myeloid-cell-specific Nlrp12-deficient mice display a heightened interferon and TNF response and are more resistant to VSV infection. These results indicate that NLRP12 functions as a checkpoint for anti-viral RIG-I activation. Chen et al. show that the nucleotide-binding domain and leucine repeat domain-containing protein NLRP12 associates with the ubiquitin ligase TRIM25 to reduce K63-linked ubiquitination of the anti-viral innate immune receptor RIG-I. This prevents RIG-I association with MAVS and thus serves as a checkpoint for interferon and cytokine induction in response to RNA viruses.
Monte Carlo Tree Search based Hybrid Optimization of Variational Quantum Circuits
Creators: name: Yao, Jiahao
name: Li, Haoya
name: Bukov, Marin
name: Lin, Lin
name: Ying, Lexing
Publisher: name: arXiv
Year: 2022
Subjects: subject: Quantum Physics (quant-ph)
subject: Quantum Gases (cond-mat.quant-gas)
subject: Machine Learning (cs.LG)
subject: Computational Physics (physics.comp-ph)
subject: FOS: Physical sciences
subject: FOS: Computer and information sciences

description: Variational quantum algorithms stand at the forefront of simulations on near-term and future fault-tolerant quantum devices. While most variational quantum algorithms involve only continuous optimization variables, the representational power of the variational ansatz can sometimes be significantly enhanced by adding certain discrete optimization variables, as is exemplified by the generalized quantum approximate optimization algorithm (QAOA). However, the hybrid discrete-continuous optimization problem in the generalized QAOA poses a challenge to the optimization. We propose a new algorithm called MCTS-QAOA, which combines a Monte Carlo tree search method with an improved natural policy gradient solver to optimize the discrete and continuous variables in the quantum circuit, respectively. We find that MCTS-QAOA has excellent noise-resilience properties and outperforms prior algorithms in challenging instances of the generalized QAOA.
Fahrerintentionserkennung zur lichtbasierten Kommunikation mit Fußgängern
Creators: name: Reschke, Johannes
Publisher: name: KIT Scientific Publishing
Year: 2022
Subjects: Fahrzeug-Fußgänger-Kommunikation
Symbole
Farben
Neuronale Netze
Automatisiertes Fahren
Vehicle-Pedestrian-Communication
Symbols
Colors
Neural Networks
Automated Driving

description: Besonders Fußgänger sind auf die Interaktion mit anderen Verkehrsteilnehmern angewiesen, welche durch Einführung automatisierter Fahrsysteme entfallen wird und daher zwischen Fahrzeug und Fußgänger stattfinden muss. Deshalb werden unterschiedliche Konzepte zur Fahrzeug-Fußgänger-Kommunikation evaluiert. Die Fahrerintentionserkennung ermöglicht es den Fußgängern, die neuartigen Zeichen zu erlernen, indem der Fahrer und das Fahrzeug kommunizieren.
Identification of a Locus in Mice that Regulates the Collateral Damage and Lethality of Virus Infection
Creators: name: Vick, S.C.
name: Cook, K.D.
name: Mitchell, J.E.
name: Lee, R.H.
name: Pardo-Manuel de Villena, F.
name: Lund, M.M.
name: Ting, J.P.Y.
name: Uchimura, T.
name: Misumi, I.
name: Whitmire, J.K.
name: Bergmeier, W.
name: Mieczkowski, P.
Publisher: name: Elsevier B.V.
Year: 2019

description: Arenaviruses can cause severe hemorrhagic disease in humans, which can progress to organ failure and death. The underlying mechanisms causing lethality and person-to-person variation in outcome remain incompletely explained. Herein, we characterize a mouse model that recapitulates many features of pathogenesis observed in humans with arenavirus-induced hemorrhagic disease, including thrombocytopenia, severe vascular leakage, lung edema, and lethality. The susceptibility of congenic B6.PL mice to lymphocytic choriomeningitis virus (LCMV) infection is associated with increased antiviral T cell responses in B6.PL mice compared with C57BL/6 mice and is T cell dependent. Pathogenesis imparted by the causative locus is inherited in a semi-dominant manner in F1 crosses. The locus includes PL-derived sequence variants in both poorly annotated genes and genes known to contribute to immune responses. This model can be used to further interrogate how limited genetic differences in the host can remarkably alter the disease course of viral infection.
D1.1 Preliminary versions of suspect screening and NTS analysis
Creators: name: Karlsson, Thomas Molnár
name: Tisler, Selina
name: Devers, Jason
name: Christensen, Jan H.
Publisher: name: Zenodo
Year: 2024

description: Developing standard operating protocols (SOPs) for runoff analysis – to be used both within D4RUNOFF and beyond – is among the main aims of WP1. It is an iterative process that draws on previous studies and methodologies to develop and improve workflows sample preparation, chemical analysis, data processing, and cheminformatics.This document presents the preliminary versions of suspect screening and non-target screening (NTS) workflows.

The workflows have already been tested on pilot samples collected in M3 of the project. This ensures their usefulness for runoff analysis and provides a good starting point for further developments during the project.While this draft is therefore based on extensive experience with the methodologies, each step in the workflows will be further developed during the project. Toward the end of WP1, fully detailed standard operating protocols for suspect screening and NTS will be delivered as part of D1.2 and D1.5.
Upper and lower bounds in radio networks
Creators: name: Mosteiro, Miguel
Publisher: name: No Publisher Supplied
Year: 2007

description: Sensor nodes are very weak computers that get distributed at random on a surface in order to achieve a large-scale sensing task. Once deployed, they must wake up and form a radio network. Given the extremely limited resources of sensor nodes, finding efficient solutions even for basic problems is very challenging. The results in this thesis concern the initialization from scratch, or Bootstrapping, of a Sensor Network. More precisely, we seek efficient-provable solutions to the most fundamental problem in Sensor Networks, its self organization. At the same time, we study lower bounds on the time complexity of such a problem. The first set of results in this thesis address the three parts that Sensor Network bootstrapping research has: to model the restrictions on sensor nodes; to prove that the sensors connectivity graph has a subgraph that would make a good network; and to give a distributed protocol for finding such a network subgraph that can be implemented on sensor nodes. A study of the Sensor Network Bootstrapping problem would not be complete without a study of lower bounds on the time complexity of solving it. Strikingly, the most basic problem in a Radio Network, i.e. to achieve a successful transmission, can be proved to be as difficult as other more complex problems under the constraints of a sensor node. The second set of results of this thesis shows new lower bounds for collision-free transmissions in Radio Networks. The main lower bound is tight for a variety of problems. An extension of this result gives the first lower bound for Sensor Network Bootstrapping. A lower bound on the expectation for fair protocols is also shown. Another contribuition of this thesis is a survey of research in Radio Networks. The survey includes two parts that have received extensive study: upper bounds for Sensor Network formation, and upper and lower bounds for non-colliding transmissions in Radio Networks proved under the broader context of more complex problems.
Viral DNA Binding to NLRC3, an Inhibitory Nucleic Acid Sensor, Unleashes STING, a Cyclic Dinucleotide Receptor that Activates Type I Interferon
Creators: name: Zhang, L.
name: Ting, J.P.-Y.
name: Dokholyan, N.V.
name: Petrucelli, A.S.
name: Li, X.
name: Zhang, S.
name: Zhu, C.
name: Li, P.
name: Ariel, P.
name: Tam, J.W.
name: Zhao, B.
name: Mo, J.
name: Ke, H.
name: Duncan, J.A.
name: Deng, M.
Publisher: name: Cell Press
Year: 2019

description: Immune suppression is a crucial component of immunoregulation and a subgroup of nucleotide-binding domain (NBD), leucine-rich repeat (LRR)-containing proteins (NLRs) attenuate innate immunity. How this inhibitory function is controlled is unknown. A key question is whether microbial ligands can regulate this inhibition. NLRC3 is a negative regulator that attenuates type I interferon (IFN-I) response by sequestering and attenuating stimulator of interferon genes (STING) activation. Here, we report that NLRC3 binds viral DNA and other nucleic acids through its LRR domain. DNA binding to NLRC3 increases its ATPase activity, and ATP-binding by NLRC3 diminishes its interaction with STING, thus licensing an IFN-I response. This work uncovers a mechanism wherein viral nucleic acid binding releases an inhibitory innate receptor from its target.
Protection and precariousness: workplace mobbing, gender and neoliberalism in Northern Italy
Creators: name: Mole, Noelle J.
Publisher: name: No Publisher Supplied
Year: 2007

description: This dissertation, based on fourteen months of fieldwork from 2003-2004, reveals the cultural co-production of gender, work and capitalist practices in one of Italy's economic strongholds, the northern city of Padua. The study traces and conceptualizes the emergence, institutionalization and charged circulation of "mobbing" across varied field sites: corporations, mobbing clinics and state public health institutions. On one level, mobbing refers to a set of vexing practices that isolate, degrade and humiliate a worker to the point of his or her resignation. However, I consider mobbing a deeply gendered cultural discourse about the intensified precariousness of labor that shapes and reflects the desires and subjectivities of Italians during neoliberal reform. I argue that programs to expand Italy's neoliberal economy and promote market flexibility collide with welfare state laws that safeguard employment in ways that make mobbing a particularly salient issue in Italy. That mobbing emerges between a precarious labor market and state protections, in turn, produces complex and opposing effects and paradoxes for workers. Far from envisioning protection and precariousness as two impenetrable categories, I aim to unveil how certain labor and state protections actually intensify the precariousness of workers. I also show how within social and economic precariousness worker-citizens find new pathways for protection. The "cultural biography" of mobbing pertains to a critical historical moment beginning in the late twentieth century when labor rights, good health and job protections come most vividly into direct opposition with a set of social, economic and political risks and uncertainties. I reveal how it is precisely the volatile simultaneity between protection and precariousness--fueled by apprehension and risk in the workplace--that produces mobbing as a culturally urgent issue and source of embodied identity in Italy. My study, delving into the charged life of mobbing, lends insight into how social actors produce meaning in a period of neoliberal reform, as well as how the intimacies of affect, health and gendered relations are inextricably articulated with the state and global economic processes.
Stochastic exciton-scattering theory of optical lineshapes: Renormalized many-body contributions
Creators: name: Li, Hao
name: Shah, S. A.
name: Bittner, Eric R.
name: Piryatinski, Andrei
name: Silva, Carlos
Publisher: name: arXiv
Year: 2022
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Other Condensed Matter (cond-mat.other)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: Spectral line-shapes provide a window into the local environment coupled to a quantum transition in the condensed phase. In this paper, we build upon a stochastic model to account for non-stationary background processes produced by broad-band pulsed laser stimulation. In particular, we consider the contribution of pair-fluctuations arising from the full bosonic many-body Hamiltonian within a mean-field approximation, treating the coupling to the system as a stochastic noise term. Using the It{ô} transformation, we consider two limiting cases for our model which lead to a connection between the observed spectral fluctuations and the spectral density of the environment. In the first case, we consider a Brownian environment and show that this produces spectral dynamics that relax to form dressed excitonic states and recover an Anderson-Kubo-like form for the spectral correlations. In the second case, we assume that the spectrum is Anderson-Kubo like, and invert to determine the corresponding background. Using the Jensen inequality, we obtain an upper limit for the spectral density for the background. The results presented here provide the technical tools for applying the stochastic model to a broad range of problems.
description: Replaces previous incorrect posting. In press, J. Chem. Phys
Classification of Commutator Algebras Leading to the New Type of Closed Baker-Campbell-Hausdorff Formulas
Creators: name: Matone, Marco
Publisher: name: arXiv
Year: 2015
Subjects: subject: Mathematical Physics (math-ph)
subject: High Energy Physics - Theory (hep-th)
subject: Representation Theory (math.RT)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences
subject: FOS: Mathematics

description: We show that there are {\it 13 types} of commutator algebras leading to the new closed forms of the Baker-Campbell-Hausdorff (BCH) formula $$\exp(X)\exp(Y)\exp(Z)=\exp({AX+BZ+CY+DI}) \ , $$ derived in arXiv:1502.06589, JHEP {\bf 1505} (2015) 113. This includes, as a particular case, $\exp(X) \exp(Z)$, with $[X,Z]$ containing other elements in addition to $X$ and $Z$. The algorithm exploits the associativity of the BCH formula and is based on the decomposition $\exp(X)\exp(Y)\exp(Z)=\exp(X)\exp({αY}) \exp({(1-α) Y}) \exp(Z)$, with $α$ fixed in such a way that it reduces to $\exp({\tilde X})\exp({\tilde Y})$, with $\tilde X$ and $\tilde Y$ satisfying the Van-Brunt and Visser condition $[\tilde X,\tilde Y]=\tilde u\tilde X+\tilde v\tilde Y+\tilde cI$. It turns out that $e^α$ satisfies, in the generic case, an algebraic equation whose exponents depend on the parameters defining the commutator algebra. In nine {\it types} of commutator algebras, such an equation leads to rational solutions for $α$. We find all the equations that characterize the solution of the above decomposition problem by combining it with the Jacobi identity.
description: 15 pages. Typos corrected. JGP version
Two-qubit gate using conditional driving for highly detuned Kerr-nonlinear parametric oscillators
Creators: name: Chono, Hiroomi
name: Kanao, Taro
name: Goto, Hayato
Publisher: name: arXiv
Year: 2022
Subjects: subject: Quantum Physics (quant-ph)
subject: Superconductivity (cond-mat.supr-con)
subject: Applied Physics (physics.app-ph)
subject: FOS: Physical sciences

description: A Kerr-nonlinear parametric oscillator (KPO) is one of the promising devices to realize qubits for universal quantum computing. The KPO can stabilize two coherent states with opposite phases, yielding a quantum superposition called a Schrödinger cat state. Universal quantum computing with KPOs requires three kinds of quantum gates: $R_z, R_x$, and $R_{zz}$ gates. We theoretically propose a two-qubit gate $R_{zz}$ for highly detuned KPOs. In the proposed scheme, we add another two-photon drive for the first KPO. This leads to the $R_{zz}$ gate based on the driving of the second KPO depending on the first-KPO state, which we call "conditional driving." First, we perform simulations using a conventional KPO Hamiltonian derived from a superconducting-circuit model under some approximations and evaluate the gate fidelity. Next, we also perform numerical simulations of the two-qubit gate using the superconducting-circuit model without the approximations. The simulation results indicate that two-qubit gates can be implemented with high fidelity ($>99.9\%$) for rotation angles required for universality.
description: 9 pages, 7 figures
title: Waveguide for air-coupled ultrasonic phased-arrays with propagation time compensation and plug-in assembly
Creators: name: Rutsch, Matthias
name: Unger, Alexander
name: Allevato, Gianni
name: Hinrichs, Jan
name: Jäger, Axel
name: Kaindl, Thomas
name: Kupnik, Mario
Publisher: name: AIP Publishing
Year: 2024

description: Waveguides allow grating lobe free beamforming for air-coupled ultrasonic phased-arrays by reducing the effective inter-element spacing to half wavelength. Since the sound waves propagate through the waveguide ducts, additional time delays are introduced. In this work, we present analytical, numerical, and experimental methods to estimate these time delays. Afterwards, two different waveguides are compared. The first one consists of equal-length ducts, requiring a time-consuming assembly process of the ultrasonic phased-array. In contrast, the second waveguide consists of Bézier-shaped ducts of unequal lengths but a planar input port allowing fast assembly. The analytical model is based on the geometric lengths of the waveguide ducts. The numerical model relies on a transient finite element analysis. All simulations are validated in an anechoic chamber using a calibrated microphone. The analytical (7.6% deviation) and numerical (3.2% deviation) propagation time models are in good agreement with the measurements. By using the analyzed propagation times for the compensation of the unequal waveguide duct lengths, we restored the beamforming capability without significant sound pressure level (SPL) loss. This work shows the possibility of reduced transducer assembly time for waveguided air-coupled phased-arrays without a reduced SPL.
Platelet-activating factor (PAF) mediates NLRP3-NEK7 inflammasome induction independently of PAFR
Creators: name: Deng, M.
name: Golenbock, D.T.
name: Beutler, B.
name: Tam, J.W.
name: Brickey, W.J.
name: Johnson, B.M.
name: New, J.S.
name: Koller, B.H.
name: McKinnon, K.P.
name: Shi, H.
name: Ting, J.P.-Y.
name: Guo, H.
name: Lenox, A.
Publisher: name: Rockefeller University Press
Year: 2019

description: The role of lipids in inflammasome activation remains underappreciated. The phospholipid, platelet-activating factor (PAF), exerts multiple physiological functions by binding to a G protein-coupled seven-transmembrane receptor (PAFR). PAF is associated with a number of inflammatory disorders, yet the molecular mechanism underlying its proinflammatory function remains to be fully elucidated. We show that multiple PAF isoforms and PAF-like lipids can activate the inflammasome, resulting in IL-1β and IL-18 maturation. This is dependent on NLRP3, ASC, caspase-1, and NEK7, but not on NLRC4, NLRP1, NLRP6, AIM2, caspase-11, or GSDMD. Inflammasome activation by PAF also requires potassium efflux and calcium influx but not lysosomal cathepsin or mitochondrial reactive oxygen species. PAF exacerbates peritonitis partly through inflammasome activation, but PAFR is dispensable for PAF-induced inflammasome activation in vivo or in vitro. These findings reveal that PAF represents a damage-associated signal that activates the canonical inflammasome independently of PAFR and provides an explanation for the ineffectiveness of PAFR antagonist in blocking PAF-mediated inflammation in the clinic.
Responses of murine keratinocytes to oxidative stress
Creators: name: Black, Adrienne T.
Publisher: name: No Publisher Supplied
Year: 2007

description: Oxidative stress is well recognized as a major contributing factor in the development of cutaneous disease. The generation of reactive oxygen intermediates (ROI) damage cellular macromolecules, causing mutagenic DNA lesions, altered enzyme function, lipid peroxidation and inappropriate signaling. Induction of oxidative stress is associated with the onset of inflammation through production of arachidonic acid-derived lipid mediators including prostaglandins and leukotrienes although the mechanisms linking these two processes are unclear at this time. As the protective barrier of the body, the skin is exposed to many oxidants. Two such potent inducers of oxidative stress are the high energy wavelengths of the ultraviolet B (UVB) spectra (290-320 nm) and the redoxcycling herbicide paraquat (1,1'-dimethyl-4,4'-bipyridinium). In the present studies, we compared the effect of UVB and paraquat on the expression of antioxidant and arachidonic acid metabolism enzymes in undifferentiated and calcium-differentiated primary mouse keratinocytes. Using enzyme assays, we found that both UVB (2.5-25mJ/cm2) and paraquat (100 µM) generated ROI and were effective inducers of oxidative stress in these cells and that paraquat readily undergoes redox-cycling. Both agents upregulated the expression of several antioxidant enzymes, measured using realtime PCR although a greater number of enzymes were induced by paraquat. UVB and paraquat equally upregulated eicosanoid enzyme expression; these enzymes included the cyclooxygenases, prostanoid synthases, lipoxygenases and leukotriene synthetic enzymes as well as the prostaglandin and leukotriene receptors. Using HPLC with fluorescence detection, UVB was found to modulate prostaglandin production. In both cell types, UVB caused a dose-dependent activation of the p38 and JNK MAP kinases. Akt kinase, however, was found to be activated only in undifferentiated cells with constitutive phosphorylation in differentiated cells. Inhibition of these enzymes markedly inhibited mRNA expression of several eicosanoid enzymes while other enzymes other were unaffected. Taken together, these data demonstrate that UVB light and paraquat effectively induce both antioxidant and eicosanoid biosynthetic enzymes in mouse keratinocytes and that activation of these pathways are regulated by MAP and Akt kinase activity. The elucidation of the keratinocyte response to oxidative stress is a necessary step to a better understanding of the effects of oxidants on the skin.
Topological and nematic ordered phases in many-body cluster-Ising models
Creators: name: Giampaolo, S. M.
name: Hiesmayr, B. C.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We present a fully analytically solvable family of models with many-body cluster interaction and Ising interaction. This family exhibits two phases, dubbed cluster and Ising phases, respectively. The critical point turns out to be independent of the cluster size $n+2$ and is reached exactly when both interactions are equally weighted. For even $n$ we prove that the cluster phase corresponds to a nematic ordered phase and in the case of odd $n$ to a symmetry protected topological ordered phase. Though complex, we are able to quantify the multi-particle entanglement content of neighboring spins. We prove that there exists no bipartite or, in more detail, no $n+1$-partite entanglement. This is possible since the non-trivial symmetries of the Hamiltonian restrict the state space. Indeed, only if the Ising interaction is strong enough (local) genuine $n+2$-partite entanglement is built up. Due to their analytically solvableness the $n$-cluster-Ising models serve as a prototype for studying non trivial-spin orderings and due to their peculiar entanglement properties they serve as a potential reference system for the performance of quantum information tasks.
description: 10 pages, 9 figures
i-Align: an interpretable knowledge graph alignment model
Creators: name: Trisedya, Bayu Distiawan
name: Salim, Flora D
name: Chan, Jeffrey
name: Spina, Damiano
name: Scholer, Falk
name: Sanderson, Mark
Publisher: name: arXiv
Year: 2023
Subjects: subject: Artificial Intelligence (cs.AI)
subject: FOS: Computer and information sciences

description: Knowledge graphs (KGs) are becoming essential resources for many downstream applications. However, their incompleteness may limit their potential. Thus, continuous curation is needed to mitigate this problem. One of the strategies to address this problem is KG alignment, i.e., forming a more complete KG by merging two or more KGs. This paper proposes i-Align, an interpretable KG alignment model. Unlike the existing KG alignment models, i-Align provides an explanation for each alignment prediction while maintaining high alignment performance. Experts can use the explanation to check the correctness of the alignment prediction. Thus, the high quality of a KG can be maintained during the curation process (e.g., the merging process of two KGs). To this end, a novel Transformer-based Graph Encoder (Trans-GE) is proposed as a key component of i-Align for aggregating information from entities' neighbors (structures). Trans-GE uses Edge-gated Attention that combines the adjacency matrix and the self-attention matrix to learn a gating mechanism to control the information aggregation from the neighboring entities. It also uses historical embeddings, allowing Trans-GE to be trained over mini-batches, or smaller sub-graphs, to address the scalability issue when encoding a large KG. Another component of i-Align is a Transformer encoder for aggregating entities' attributes. This way, i-Align can generate explanations in the form of a set of the most influential attributes/neighbors based on attention weights. Extensive experiments are conducted to show the power of i-Align. The experiments include several aspects, such as the model's effectiveness for aligning KGs, the quality of the generated explanations, and its practicality for aligning large KGs. The results show the effectiveness of i-Align in these aspects.
description: Data Min Knowl Disc (2023)