cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Development of nanostructured lipid carriers as a promising tool for methotrexate delivery: physicochemical and in vitro evaluation
Creators: name: Rathee, Jyoti
name: Kanwar, Rohini
name: Kumari, Laxmi
name: Pawar, Sandip V.
name: Sharma, Shikha
name: Ali, Md. Ehesan
name: Salunke, Deepak B.
name: Mehta, Surinder Kumar
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biochemistry
subject: Space Science
subject: 29999 Physical Sciences not elsewhere classified
subject: FOS: Physical sciences
subject: Medicine
subject: Pharmacology
subject: Biotechnology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Cancer

description: The aim of the present study is to fabricate the stable nanostructured lipid carriers (NLCs) using biocompatible excipients for the encapsulation of Methotrexate (MTX), a chemotherapeutic agent for breast cancer treatment. MTX has restricted clinical applications owing to its low solubility, non-specific targeting and adverse side effects. Glyceryl Monostearate (GMS) and Miglyol 812 (MI1) were chosen as solid and liquid lipids, respectively, for the fabrication of NLCs, and the influence of variation of solid and liquid composition was investigated. The prepared NLCs exhibited long-term stability and spherical shape morphology as characterized by electron microscopy. The internal structure of fabricated NLCs was arranged into cubic crystalline as confirmed by small-angle X-ray scattering (SAXS) analysis. MTX's encapsulation efficiency of ∼85 ± 0.9%. and sustained in vitro release of MTX ∼ 52% ± 3.0 in 24 h was achieved. Classical molecular dynamics (MD) simulations were performed to study the structural stability of the MTX encapsulated NLCs. Hemolysis carried out on the NLCs showcased the biosafety of the formulation under the tolerance limit (<10%). Further, the MTT assay demonstrates that MTX-loaded NLCs exhibited toxicity against HeLa and MCF-7 cell lines as compared to blank NLCs. The finding demonstrates NLCs as promising vehicles for MTX delivery to address cancer. Communicated by Ramaswamy H. Sarma
The well-posedness issue for the density-dependent Euler equations in endpoint Besov spaces
Creators: name: Danchin, Raphaël
name: Fanelli, Francesco
Publisher: name: arXiv
Year: 2013
Subjects: subject: Analysis of PDEs (math.AP)
subject: FOS: Mathematics

description: This work is the continuation of the recent paper \cite{D2} devoted to the density-dependent incompressible Euler equations. Here we concentrate on the well-posedness issue in Besov spaces of type $B^s_{\infty,r}$ embedded in the set of Lipschitz continuous functions, a functional framework which contains the particular case of Hölder spaces and of the endpoint Besov space $B^1_{\infty,1}.$ For such data and under the nonvacuum assumption, we establish the local well-posedness and a continuation criterion in the spirit of that of Beale, Kato and Majda in \cite{BKM}. In the last part of the paper, we give lower bounds for the lifespan of a solution. In dimension two, we point out that the lifespan tends to infinity when the initial density tends to be a constant. This is, to our knowledge, the first result of this kind for the density-dependent incompressible Euler equations.
Three dimensional evolution of SN 1987A in a self-gravitating disk
Creators: name: Zaninetti, L.
Publisher: name: arXiv
Year: 2013
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: The introduction of a exponential or power law gradient in the interstellar medium (ISM) allows to produce an asymmetric evolution of the supernova remnant (SNR) when the framework of the thin layer approximation is adopted. Unfortunately both the exponential and power law gradients for the ISM do not have a well defined physical meaning. The physics conversely is well represented by an isothermal self-gravitating disk of particles whose velocity is everywhere Maxwellian. . We derived a law of motion in the framework of the thin layer approximation with a control parameter of the swept mass. The photon's losses ,that are often neglected in the thin layer approximation, are modeled trough a velocity dependence. The developed framework is applied to SNR 1987A and the three observed rings are simulated.
description: 11 pages and 9 figures. arXiv admin note: text overlap with arXiv:1109.4012
Review of recent developments of the functional renormalization group for systems out of equilibrium
Creators: name: Camacho, G.
name: Klöckner, C.
name: Kennes, D. M.
name: Karrasch, C.
Publisher: name: arXiv
Year: 2022
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: We recapitulate recent developments of the functional renormalization group (FRG) approach to the steady state of systems out of thermal equilibrium. In particular, we discuss second-order truncation schemes which account for the frequency-dependence of the two particle vertex and which incorporate inelastic processes. Our focus is on two different types of one-dimensional fermion chains: i) infinite, open systems which feature a translation symmetry, and ii) finite systems coupled to left and right reservoirs. In addition to giving a detailed and unified review of the technical derivation of the FRG schemes, we briefly summarize some of the key physical results. In particular, we compute the non-equilibrium phase diagram and analyze the fate of the Berezinskii-Kosterlitz-Thouless transition in the infinite, open system.
description: Appearing as part of a EPJB collection "Developments in the functional renormalization group approach to correlated electron systems"
Electromagnetic waves destabilized by runaway electrons in near-critical electric fields
Creators: name: Kómár, A.
name: Pokol, G. I.
name: Fülöp, T.
Publisher: name: arXiv
Year: 2013
Subjects: subject: Plasma Physics (physics.plasm-ph)
subject: FOS: Physical sciences

description: Runaway electron distributions are strongly anisotropic in velocity space. This anisotropy is a source of free energy that may destabilize electromagnetic waves through a resonant interaction between the waves and the energetic electrons. In this work we investigate the high-frequency electromagnetic waves that are destabilized by runaway electron beams when the electric field is close to the critical field for runaway acceleration. Using a runaway electron distribution appropriate for the near-critical case we calculate the linear instability growth rate of these waves and conclude that the obliquely propagating whistler waves are most unstable. We show that the frequencies, wave numbers and propagation angles of the most unstable waves depend strongly on the magnetic field. Taking into account collisional and convective damping of the waves, we determine the number density of runaways that is required to destabilize the waves and show its parametric dependences.
description: 22 pages, 11 figures, to be published in Physics of Plasmas
PSSTRNet: Progressive Segmentation-guided Scene Text Removal Network
Creators: name: Lyu, Guangtao
name: Zhu, Anna
Publisher: name: arXiv
Year: 2023
Subjects: subject: Computer Vision and Pattern Recognition (cs.CV)
subject: FOS: Computer and information sciences

description: Scene text removal (STR) is a challenging task due to the complex text fonts, colors, sizes, and background textures in scene images. However, most previous methods learn both text location and background inpainting implicitly within a single network, which weakens the text localization mechanism and makes a lossy background. To tackle these problems, we propose a simple Progressive Segmentation-guided Scene Text Removal Network(PSSTRNet) to remove the text in the image iteratively. It contains two decoder branches, a text segmentation branch, and a text removal branch, with a shared encoder. The text segmentation branch generates text mask maps as the guidance for the regional removal branch. In each iteration, the original image, previous text removal result, and text mask are input to the network to extract the rest part of the text segments and cleaner text removal result. To get a more accurate text mask map, an update module is developed to merge the mask map in the current and previous stages. The final text removal result is obtained by adaptive fusion of results from all previous stages. A sufficient number of experiments and ablation studies conducted on the real and synthetic public datasets demonstrate our proposed method achieves state-of-the-art performance. The source code of our work is available at: \href{https://github.com/GuangtaoLyu/PSSTRNet}{https://github.com/GuangtaoLyu/PSSTRNet.}
description: Accepted by ICME2022
On the Calculation of the Variance of Algebraic Variables in Power System Dynamic Models with Stochastic Processes
Creators: name: Adeen, Muhammad
name: Bizzarri, Federico
name: del Giudice, Davide
name: Grillo, Samuele
name: Linaro, Daniele
name: Brambilla, Angelo
name: Milano, Federico
Publisher: name: arXiv
Year: 2022
Subjects: subject: Systems and Control (eess.SY)
subject: FOS: Electrical engineering, electronic engineering, information engineering

description: This letter presents a technique to calculate the variance of algebraic variables of power system models represented as a set of stochastic differential-algebraic equations. The technique utilizes the solution of a Lyapunov equation and requires the calculation of the state matrix of the system. The IEEE 14-bus system serves to demonstrate the accuracy of the proposed technique over a wide range of variances of stochastic processes. The accuracy is evaluated by comparing the results with those obtained with Monte Carlo time domain simulations. Finally, a case study based on a 1479-bus dynamic model of the all-island Irish transmission system shows the computational efficiency of the proposed approach compared to the Monte Carlo method.
In silico molecular docking study of Andrographis paniculata phytochemicals against TNF-α as a potent anti-rheumatoid drug
Creators: name: Tarachand, Sharma Pooja
name: Thirumoorthy, Gopishankar
name: Lakshmaiah, Vasantha Veerappa
name: Nagella, Praveen
Publisher: name: Taylor & Francis
Year: 2022
Subjects: subject: Biophysics
subject: Biochemistry
subject: Cell Biology
subject: Pharmacology
subject: Biotechnology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Ecology
subject: FOS: Biological sciences
subject: Immunology
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: Cancer

description: Tumor necrosis factor-α (TNF-α) is a proinflammatory cytokine which plays a crucial role in controlling inflammatory responses. The pathway of Rheumatoid arthritis (RA) leading to TNF-alpha is activated by macrophages and quite often by natural killer cells and lymphocytes. In the inflammatory phase, it is believed to be the main mediator and to be anchored with the progression of different diseases such as ankylosing spondylitis, Crohn's disease, and Rheumatoid arthritis (RA). The major goal of this study is to use in silico docking studies to investigate the anti-inflammatory potential of a bioactive molecule from the medicinal plant Andrographis paniculata. The three-dimensional structures of different phytochemicals of A. paniculata were obtained from PubChem database, and the receptor protein was derived from PDB database. Docking analysis was executed using AutoDock vina, and the binding energies were compared. Bisandrographolide A and Andrographidine C revealed the highest score of −8.6 Kcal/mol, followed by, Neoandrographolide (−8.5 Kcal/mol). ADME and toxicity parameters were evaluated for these high scoring ligands and results showed that Andrographidine C could be a potent drug, whereas Neoandrographolide and Bisandrographolide A can be modified in in vitro and can lead to a promising drug. Further, the top scorer (Andrographidine C) and control drug (Leflunomide) were subjected to 100 ns MD Simulation. The protein complex with Andrographidine C had more stable confirmation with lower RMSD (0.28 nm) and higher binding energy (−133.927 +/− 13.866 kJ/mol). In conclusion, Andrographidine C may be a potent surrogate to the disease-modifying anti-rheumatic drugs (DMARD’s) & Non-steroidal anti-inflammatory drugs (NSAID’s) that has fewer or minor adverse effects and can aid in RA management.
Adversarial Capsule Networks for Romanian Satire Detection and Sentiment Analysis
Creators: name: Echim, Sebastian-Vasile
name: Smădu, Răzvan-Alexandru
name: Avram, Andrei-Marius
name: Cercel, Dumitru-Clementin
name: Pop, Florin
Publisher: name: arXiv
Year: 2023
Subjects: subject: Computation and Language (cs.CL)
subject: FOS: Computer and information sciences

description: Satire detection and sentiment analysis are intensively explored natural language processing (NLP) tasks that study the identification of the satirical tone from texts and extracting sentiments in relationship with their targets. In languages with fewer research resources, an alternative is to produce artificial examples based on character-level adversarial processes to overcome dataset size limitations. Such samples are proven to act as a regularization method, thus improving the robustness of models. In this work, we improve the well-known NLP models (i.e., Convolutional Neural Networks, Long Short-Term Memory (LSTM), Bidirectional LSTM, Gated Recurrent Units (GRUs), and Bidirectional GRUs) with adversarial training and capsule networks. The fine-tuned models are used for satire detection and sentiment analysis tasks in the Romanian language. The proposed framework outperforms the existing methods for the two tasks, achieving up to 99.08% accuracy, thus confirming the improvements added by the capsule layers and the adversarial training in NLP approaches.
description: 15 pages, 3 figures, Accepted by NLDB 2023
Development of nanostructured lipid carriers as a promising tool for methotrexate delivery: physicochemical and in vitro evaluation
Creators: name: Rathee, Jyoti
name: Kanwar, Rohini
name: Kumari, Laxmi
name: Pawar, Sandip V.
name: Sharma, Shikha
name: Ali, Md. Ehesan
name: Salunke, Deepak B.
name: Mehta, Surinder Kumar
Publisher: name: Taylor & Francis
Year: 2022
Subjects: subject: Biochemistry
subject: Space Science
subject: 29999 Physical Sciences not elsewhere classified
subject: FOS: Physical sciences
subject: Medicine
subject: Pharmacology
subject: Biotechnology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Cancer

description: The aim of the present study is to fabricate the stable nanostructured lipid carriers (NLCs) using biocompatible excipients for the encapsulation of Methotrexate (MTX), a chemotherapeutic agent for breast cancer treatment. MTX has restricted clinical applications owing to its low solubility, non-specific targeting and adverse side effects. Glyceryl Monostearate (GMS) and Miglyol 812 (MI1) were chosen as solid and liquid lipids, respectively, for the fabrication of NLCs, and the influence of variation of solid and liquid composition was investigated. The prepared NLCs exhibited long-term stability and spherical shape morphology as characterized by electron microscopy. The internal structure of fabricated NLCs was arranged into cubic crystalline as confirmed by small-angle X-ray scattering (SAXS) analysis. MTX's encapsulation efficiency of ∼85 ± 0.9%. and sustained in vitro release of MTX ∼ 52% ± 3.0 in 24 h was achieved. Classical molecular dynamics (MD) simulations were performed to study the structural stability of the MTX encapsulated NLCs. Hemolysis carried out on the NLCs showcased the biosafety of the formulation under the tolerance limit (<10%). Further, the MTT assay demonstrates that MTX-loaded NLCs exhibited toxicity against HeLa and MCF-7 cell lines as compared to blank NLCs. The finding demonstrates NLCs as promising vehicles for MTX delivery to address cancer. Communicated by Ramaswamy H. Sarma
Transmitting signals over interstellar distances: Three approaches compared in the context of the Drake equation
Creators: name: Arnold, Luc
Publisher: name: arXiv
Year: 2013
Subjects: subject: Earth and Planetary Astrophysics (astro-ph.EP)
subject: FOS: Physical sciences

description: I compare three methods for transmitting signals over interstellar distances: radio transmitters, lasers and artificial transits. The quantitative comparison is based on physical quantities depending on energy cost and transmitting time L, the last parameter in the Drake equation. With our assumptions, radio transmitters are the most energy-effective, while macro-engineered planetary-sized objects producing artificial transits seem effective on the long term to transmit an attention-getting signal for a time that might be much longer than the lifetime of the civilization that produced the artifact.
description: Accepted for publication in the International Journal of Astrobiology, special issue on the Drake equation. http://journals.cambridge.org/action/displayJournal?jid=IJA
Molecular evolution and structural analyses of the spike glycoprotein from Brazilian SARS-CoV-2 genomes: the impact of selected mutations
Creators: name: Ferrareze, Patrícia Aline Gröhs
name: Zimerman, Ricardo Ariel
name: Franceschi, Vinícius Bonetti
name: Caldana, Gabriel Dickin
name: Netz, Paulo Augusto
name: Thompson, Claudia Elizabeth
Publisher: name: Taylor & Francis
Year: 2022
Subjects: subject: Biochemistry
subject: Molecular Biology
subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: 60506 Virology

description: The COVID-19 pandemic caused by SARS-CoV-2 has reached by February 2022 more than 380 million cases and 5.5 million deaths worldwide since its beginning in late 2019, leading to enhanced concern in the scientific community and the general population. One of the most important pieces of this host-pathogen interaction is the spike protein, which binds to the hACE2 cell receptor, mediates the membrane fusion and is the major target of neutralizing antibodies against SARS-CoV-2. The multiple amino acid substitutions observed in this region, specially in RBD have enhanced the hACE2 binding affinity and led to several modifications in the mechanisms of SARS-CoV-2 pathogenesis, improving the viral fitness and/or promoting immune evasion, with potential impact in the vaccine development. In this work, we identified 48 sites under selective pressures, 17 of them with the strongest evidence by the HyPhy tests, including VOC related mutation sites 138, 142, 222, 262, 484, 681, and 845, among others. The coevolutionary analysis identified 28 sites found not to be conditionally independent, such as E484K-N501Y. The molecular dynamics and free energy estimates showed the structural stabilizing effect and the higher impact of E484K for enhanced binding affinity between the spike RBD and hACE2 in P.1 and P.2 lineages (specially with L452V). Structural changes were also identified in the hACE molecule when interacting with B.1.1.7 RDB. Despite some destabilizing substitutions, a stabilizing effect was identified for the majority of the positively selected mutations. Communicated by Ramaswamy H. Sarma
Quantum Optics as Applied Quantum Electrodynamics is back in town
Creators: name: Stammer, Philipp
name: Lewenstein, Maciej
Publisher: name: arXiv
Year: 2023
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We start this short note by remembering the beginnings of the Warsaw School of Quantum Optics, evidently stimulated by Iwo Bialynicki-Birula at the Warsaw University, and then Centre for Theoretical Physics of Polish Academy of Sciences, and Adam Kujawski and Zofia Bialynicka-Birula at the Institute of Physics of Polish Academy of Sciences. In the theoretical approaches of the Warsaw School Quantum Field Theory was always present, and Quantum Optics was considered to be Applied Quantum Electrodynamics (QED). All of us who grew up in this fantastic community have carried and are still carrying the gospel to others. In particular, now QED began her run on the red carpet of Super Instense Laser Matter Interactions, Attosecond-physics, and Ultrafast Laser Physics, in general. We will elaborate on the recent progress in this direction, and on the open questions towards future investigations. This paper celebrates the 90th birthday of Prof. Iwo Bialynicki-Birula, our QED guru!
description: This article belongs to the special issue of Acta Physica Polonica A printed in honor of Professor Iwo Bialynicki-Birula on the occasion of his 90th birthday (Ed. Tomasz Sowinski, DOI:10.12693/APhysPolA.143.S0)
Additive Causal Bandits with Unknown Graph
Creators: name: Malek, Alan
name: Aglietti, Virginia
name: Chiappa, Silvia
Publisher: name: arXiv
Year: 2023
Subjects: subject: Machine Learning (cs.LG)
subject: Machine Learning (stat.ML)
subject: FOS: Computer and information sciences

description: We explore algorithms to select actions in the causal bandit setting where the learner can choose to intervene on a set of random variables related by a causal graph, and the learner sequentially chooses interventions and observes a sample from the interventional distribution. The learner's goal is to quickly find the intervention, among all interventions on observable variables, that maximizes the expectation of an outcome variable. We depart from previous literature by assuming no knowledge of the causal graph except that latent confounders between the outcome and its ancestors are not present. We first show that the unknown graph problem can be exponentially hard in the parents of the outcome. To remedy this, we adopt an additional additive assumption on the outcome which allows us to solve the problem by casting it as an additive combinatorial linear bandit problem with full-bandit feedback. We propose a novel action-elimination algorithm for this setting, show how to apply this algorithm to the causal bandit problem, provide sample complexity bounds, and empirically validate our findings on a suite of randomly generated causal models, effectively showing that one does not need to explicitly learn the parents of the outcome to identify the best intervention.
Numerically exact correlations and sampling in the two-dimensional Ising spin glass
Creators: name: Thomas, Creighton K.
name: Middleton, A. Alan
Publisher: name: arXiv
Year: 2013
Subjects: subject: Disordered Systems and Neural Networks (cond-mat.dis-nn)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: A powerful existing technique for evaluating statistical mechanical quantities in two-dimensional Ising models is based on constructing a matrix representing the nearest neighbor spin couplings and then evaluating the Pfaffian of the matrix. Utilizing this technique and other more recent developments in evaluating elements of inverse matrices and exact sampling, a method and computer code for studying two-dimensional Ising models is developed. The formulation of this method is convenient and fast for computing the partition function and spin correlations. It is also useful for exact sampling, where configurations are directly generated with probability given by the Boltzmann distribution. These methods apply to Ising model samples with arbitrary nearest-neighbor couplings and can also be applied to general dimer models. Example results of computations are described, including comparisons with analytic results for the ferromagnetic Ising model, and timing information is provided.
description: 18 pp., 8 figures, 1 table, includes code as supplemental material
Report on computational assessment of tumor infiltrating lymphocytes from the International Immuno-Oncology Biomarker Working Group
Creators: name: Amgad, M
name: Stovgaard, ES
name: Balslev, E
name: Thagaard, J
name: Chen, W
name: Dudgeon, S
name: Sharma, A
name: Kerner, JK
name: Denkert, C
name: Yuan, Y
name: AbdulJabbar, K
name: Wienert, S
name: Savas, P
name: Voorwerk, L
name: Beck, AH
name: Madabhushi, A
name: Hartman, J
name: Sebastian, MM
name: Horlings, HM
name: Hudeček, J
name: Ciompi, F
name: Moore, DA
name: Singh, R
name: Roblin, E
name: Balancin, ML
name: Mathieu, MC
name: Lennerz, JK
name: Kirtani, P
name: Chen, IC
name: Braybrooke, JP
name: Pruneri, G
name: Demaria, S
name: Adams, S
name: Schnitt, SJ
name: Lakhani, SR
name: Rojo, F
name: Comerma, L
name: Badve, SS
name: Khojasteh, M
name: Symmans, WF
name: Sotiriou, C
name: Gonzalez-Ericsson, P
name: Pogue-Geile, KL
name: Kim, RS
name: Rimm, DL
name: Viale, G
name: Hewitt, SM
name: Bartlett, JMS
name: Penault-Llorca, F
name: Goel, S
name: Lien, HC
name: Loibl, S
name: Kos, Z
name: Loi, S
name: Hanna, MG
name: Michiels, S
name: Kok, M
name: Nielsen, TO
name: Lazar, AJ
name: Bago-Horvath, Z
name: Kooreman, LFS
name: van der Laak, JAWM
name: Saltz, J
name: Gallas, BD
name: Kurkure, U
name: Barnes, M
name: Salgado, R
name: Cooper, LAD
name: Group, International Immuno-Oncology Biomarker Working
Publisher: name: The Francis Crick Institute
Year: 2023
Subjects: Tumour Biology
Signalling & Oncogenes
Genetics & Genomics
Genome Integrity & Repair
Human Biology & Physiology
Chemical Biology & High Throughput
Ecology,Evolution & Ethology
Computational & Systems Biology

description: Assessment of tumor-infiltrating lymphocytes (TILs) is increasingly recognized as an integral part of the prognostic workflow in triple-negative (TNBC) and HER2-positive breast cancer, as well as many other solid tumors. This recognition has come about thanks to standardized visual reporting guidelines, which helped to reduce inter-reader variability. Now, there are ripe opportunities to employ computational methods that extract spatio-morphologic predictive features, enabling computer-aided diagnostics. We detail the benefits of computational TILs assessment, the readiness of TILs scoring for computational assessment, and outline considerations for overcoming key barriers to clinical translation in this arena. Specifically, we discuss: 1. ensuring computational workflows closely capture visual guidelines and standards; 2. challenges and thoughts standards for assessment of algorithms including training, preanalytical, analytical, and clinical validation; 3. perspectives on how to realize the potential of machine learning models and to overcome the perceptual and practical limits of visual scoring.
Schwinger, ltd: Loop-tree duality in the parametric representation
Creators: name: Berghoff, Marko
Publisher: name: arXiv
Year: 2022
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: Mathematical Physics (math-ph)
subject: FOS: Physical sciences
subject: 81T18, 81Q30, 14D21, 52B05, 53Z05

description: We derive a variant of the loop-tree duality for Feynman integrals in the Schwinger parametric representation. This is achieved by decomposing the integration domain into a disjoint union of cells, one for each spanning tree of the graph under consideration. Each of these cells is the total space of a fiber bundle with contractible fibers over a cube. Loop-tree duality emerges then as the result of first decomposing the integration domain, then integrating along the fibers of each fiber bundle. As a byproduct we obtain a new proof that the moduli space of graphs is homotopy equivalent to its spine. In addition, we outline a potential application to Kontsevich's graph (co-)homology.
description: 25 pages. Final version
iota Horologi, the first coronal activity cycle in a young solar-like star
Creators: name: Sanz-Forcada, J.
name: Stelzer, B.
name: Metcalfe, T. S.
Publisher: name: arXiv
Year: 2013
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: Earth and Planetary Astrophysics (astro-ph.EP)
subject: FOS: Physical sciences

description: Context: The shortest chromospheric (Ca II H&K) activity cycle (1.6 yr) has been recently discovered in the young (~600 Myr) solar-like star iota Hor. Coronal X-ray activity cycles have only been discovered in a few stars other than the Sun, all of them with an older age and a lower activity level than iota Hor. Aims: We intended to find the X-ray coronal counterpart of the chromospheric cycle for i Hor. This represents the first X-ray cycle observed in an active star, as well as the paradigm of the first coronal cycles in the life of a solar-like star. Methods: We monitored i Hor with XMM-Newton observations spanning almost two years. The spectra of each observation are fit with two-temperature coronal models to study the long-term variability of the star. Results: We find a cyclic behavior in X-rays very similar to the contemporaneous chromospheric cycle. The continuous chromospheric monitoring for more than three cycle lengths shows a trend toward decreasing amplitude, apparently modulated by a longer term trend. The second cycle is disrupted prior to reaching its maximum, followed by a brief episode of chaotic variability before the cyclic behavior resumes, only to be disrupted again after slightly more than one cycle. Conclusions: We confirm the presence of an activity cycle of ~1.6 yr in i Hor both in X-rays and Ca II H&K. It is likely subject to the modulation of a longer, not yet constrained second cycle. The 1.6 yr cycle is the shortest coronal one observed to date, and i Hor represents the most active star for which a coronal activity cycle has been found. This cycle is probably representative of the first coronal cycles in the life of a solar-like star, at the age when life started on Earth.
description: Published in A&A letters. 5 pages, 3 figures, 2 tables. Press release at: http://www.cab.inta-csic.es/en/noticias/93/los-ciclos-de-las-estrellas-y-el-inicio-de-la-vida
A New Cluster of Galaxies towards the Galactic Bulge, Suzaku J1759-3450
Creators: name: Mori, Hideyuki
name: Maeda, Yoshitomo
name: Furuzawa, Akihiro
name: Haba, Yoshito
name: Ueda, Yoshihiro
Publisher: name: arXiv
Year: 2013
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: We observed an extended X-ray source designated as Suzaku J1759-3450 with the Suzaku and Chandra observations towards 1RXS J175911.0-344921, which is an unidentified X-ray source listed in the ROSAT Bright Source Catalogue. A conspicuous emission line at 6 keV was also found in the Suzaku J1759-3450 spectrum. Assuming the emission line to be K emission from He-like Fe ions, we inferred Suzaku J1759-3450 to be an extragalactic object located at z = 0.13. The radial profile of the surface brightness in the 0.5-10 keV band was explained well with an isothermal beta-model of r_c = 1.61' and beta = 0.78. The X-ray spectrum was well reproduced by an optically-thin thermal plasma with the electron temperature of kT_e = 5.3 keV attenuated by the photoelectric absorption of N_H = 2.3 x 10^21 cm^-2. The bolometric X-ray luminosity of L_X (r < r_500) = 4.3 x 10^44 erg s^-1 is consistent with that expected from the L_X-T relation of clusters of galaxies. In terms of the spatial extent, the X-ray spectrum, and the bolometric luminosity of the X-ray emitting gas, we concluded that Suzaku J1759-3450 is a new cluster of galaxies.
description: 7 pages, 4 figures, accepted for publication in PASJ
A sequence space search engine for computational protein design to modulate molecular functionality
Creators: name: Malik, Ayush
name: Banerjee, Anupam
name: Pal, Abantika
name: Mitra, Pralay
Publisher: name: Taylor & Francis
Year: 2022
Subjects: subject: Biophysics
subject: Biochemistry
subject: Genetics
subject: FOS: Biological sciences
subject: Biotechnology
subject: Evolutionary Biology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences

description: De-novo protein design explores the untapped sequence space that is otherwise less discovered during the evolutionary process. This necessitates an efficient sequence space search engine for effective convergence in computational protein design. We propose a greedy simulated annealing-based Monte-Carlo parallel search algorithm for better sequence-structure compatibility probing in protein design. The guidance provided by the evolutionary profile, the greedy approach, and the cooling schedule adopted in the Monte Carlo simulation ensures sufficient exploration and exploitation of the search space leading to faster convergence. On evaluating the proposed algorithm, we find that a dataset of 76 target scaffolds report an average root-mean-square-deviation (RMSD) of 1.07 Å and an average TM-Score of 0.93 with the modeled designed protein sequences. High sequence recapitulation of 48.7% (59.4%) observed in the design sequences for all (hydrophobic) solvent-inaccessible residues again establish the goodness of the proposed algorithm. A high (93.4%) intra-group recapitulation of hydrophobic residues in the solvent-inaccessible region indicates that the proposed protein design algorithm preserves the core residues in the protein and provides alternative residue combinations in the solvent-accessible regions of the target protein. Furthermore, a COFACTOR-based protein functional analysis shows that the design sequences exhibit altered molecular functionality and introduce new molecular functions compared to the target scaffolds. Communicated by Ramaswamy H. Sarma
title: Das „Konzil“ in Konstanz. Vom Kaufhaus zur Stadthalle
Creators: name: King, Stefan
Publisher: name: University Library Heidelberg
Year: 2015

description: Denkmalpflege in Baden-Württemberg – Nachrichtenblatt der Landesdenkmalpflege, Bd. 44, Nr. 2 (2015), Beginn und Erscheinungsfrequenz: Ausgaben pro Band: 4
$M_W$, Dark Matter and $a_μ$ in the NMSSM
Creators: name: Domingo, Florian
name: Ellwanger, Ulrich
name: Hugonie, Cyril
Publisher: name: arXiv
Year: 2022
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: High Energy Physics - Experiment (hep-ex)
subject: FOS: Physical sciences

description: We study regions in the parameter space of the NMSSM which are able to simultaneously explain the current measured values for the $W$ mass $M_W$ and the muon anomalous magnetic moment $a_μ$, and provide a dark matter relic density consistent with the observations as well as constraints from detection experiments. The corresponding regions feature light charginos, sleptons and staus in the 100-800~GeV range, at least some of them with masses below 150~GeV such that the electroweakly-interacting SUSY particles generate sufficiently large contributions to $M_W$. The LSP is always singlino-like with a mass below 140~GeV, and could possibly remain invisible even at future detection experiments. Decays of electroweak sparticles proceed through cascades via staus and/or sleptons which makes their detection challenging. We propose benchmark points for future searches of such sparticles. The lightest CP-even scalar may have a mass in the 95-98~GeV range with, however, modest signal rates in view of the mild excesses reported in this range at LEP and by CMS at the LHC.
description: 8 pages, 6 figures, references added, figures improved, SLHA files of bench mark points added as ancillary files
title: Denkmalpflegerische Themen im Unterricht etablieren. „Erlebniskoffer Historische Weinberge“. Unterrichtsmaterial der Landesdenkmalpflege für die Grundschule
Creators: name: Jacobs, Friedrich
name: Plein, Irene
name: Schrade, Barbara
Publisher: name: University Library Heidelberg
Year: 2015

description: Denkmalpflege in Baden-Württemberg – Nachrichtenblatt der Landesdenkmalpflege, Bd. 44, Nr. 2 (2015), Beginn und Erscheinungsfrequenz: Ausgaben pro Band: 4
Extracting nuclear matter properties from the neutron star matter equation of state using deep neural networks
Creators: name: Ferreira, Márcio
name: Carvalho, Valéria
name: Providência, Constança
Publisher: name: arXiv
Year: 2022
Subjects: subject: Nuclear Theory (nucl-th)
subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: The extraction of the nuclear matter properties from neutron star (NS) observations is nowadays an important issue, in particular, the properties that characterize the symmetry energy which are essential to describe correctly asymmetric nuclear matter. We use deep neural networks (DNNs) to map the relation between cold $β$-equilibrium NS matter and the nuclear matter properties. Assuming a quadratic dependence on the isospin asymmetry for the energy per particle of homogeneous nuclear matter and using a Taylor expansion up to fourth order in the iso-scalar and iso-vector contributions, we generate a dataset of different realizations of $β$-equilibrium NS matter and the corresponding nuclear matter properties. The DNN model was successfully trained, attaining great accuracy in the test set. Finally, a real case scenario was used to test the DNN model, where a set of 33 nuclear models, obtained within a relativistic mean field approach or a Skyrme force description, were fed into the DNN model and the corresponding nuclear matter parameters recovered with considerable accuracy, in particular, the standard deviations $σ(L_{\text{sym}})= 12.85$ MeV and $σ(K_{\text{sat}})= 41.02$ MeV were obtained, respectively, for the slope of the symmetry energy and the nuclear matter incompressibility at saturation.
description: 10 pages, 5 figures; published version
title: Denkmalpflegerische Themen im Unterricht etablieren. Unterrichtsmodul „Historische Ortskerne“. Unterrichtsmaterial für die Grundschule
Creators: name: Schick, Christiane
Publisher: name: University Library Heidelberg
Year: 2015

description: Denkmalpflege in Baden-Württemberg – Nachrichtenblatt der Landesdenkmalpflege, Bd. 44, Nr. 2 (2015), Beginn und Erscheinungsfrequenz: Ausgaben pro Band: 4
In silico evaluation of binding of phytochemicals from bayati (Anamirta cocculus Linn) to the glutathione-s-transferase of Asian Corn Borer (Ostrinia furnacalis Guenée)
Creators: name: Castrosanto, Melvin A.
name: Abrera, Annabelle T.
name: Manalo, Marlon N.
name: Ghosh, Arabinda
Publisher: name: Taylor & Francis
Year: 2022
Subjects: subject: Biophysics
subject: Biochemistry
subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Biotechnology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Ecology
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: Plant Biology
subject: Computational Biology

description: Asian corn borer (ACB) is a destructive insect pest of corn and causes up to 80% yield reduction in the Philippines. Synthetic insecticides have been used to control ACB but they pose a risk to human health and the environment. The use of synergists increases insecticide effectiveness and decreases the frequency of insecticide application. In line with this principle, we performed in silico screening of phytochemicals from bayati against glutathione-s-transferase (GST), one of the important detoxifying enzymes of ACB. Homology modeling was done to generate an acceptable three-dimensional protein structure (OfGST). Through ensemble molecular docking, we found that three phytosterols (stigmasterol, lupeol, and gamma-sitosterol) from bayati have a higher binding affinity to OfGST than glutathione, its natural substrate. Molecular dynamics simulation revealed that lupeol and gamma-sitosterol have a greater stabilizing effect on OfGST than stigmasterol, as supported by the RMSD, radius of gyration, and SASA plots of all complexes. Communicated by Ramaswamy H. Sarma
Creating a CLOUDY Compatible Database with CHIANTI version 10 Data
Creators: name: Gunasekera, Chamani M.
name: Chatzikos, Marios
name: Ferland, Gary J.
Publisher: name: arXiv
Year: 2022
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: Atomic and molecular data are required to conduct detailed calculations of microphysical processes performed by CLOUDY to predict the spectra of a theoretical model. One of the three databases CLOUDY currently utilizes is CHIANTI version 7.1. CHIANTI version 10.0.1 is available, but its format has changed. CLOUDY is incompatible with the newer version. We have developed a script to convert the version 10.0.1 database into its version 7.1 format so that CLOUDY does not have to change every time there is a new CHIANTI version with an evolved format. This study outlines the steps taken by the script for this version format change. We have also found a modest number of significant changes to spectral line intensities/luminosities calculated by CLOUDY with the adoption of CHIANTI version 10.0.1. These changes are a result of improvements to collision strength data.
description: 16 pages, 7 figures
Unraveling the possible inhibitors for Chorismate synthase to combat tuberculosis using in silico approach
Creators: name: Hanif, Muhammad
name: Khan, Sara
name: Farooq, Umar
name: Nouroz, Faisal
name: Sarwar, Rizwana
Publisher: name: Taylor & Francis
Year: 2022
Subjects: subject: Biophysics
subject: Biochemistry
subject: Molecular Biology
subject: Pharmacology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: Cancer
subject: 110309 Infectious Diseases
subject: FOS: Health sciences

description: Tuberculosis antibiotic resistance is a huge concern to the global population. The goal of this study was to find new and effective compounds to treat multidrug-resistant tuberculosis by targeting Chorismate synthase (CS), a crucial enzyme for Mycobacterium tuberculosis survival (MbT). The potential of a library of compounds as selective anti - tuberculosis drugs was investigated. Docking was first conducted using MoE to determine the effectiveness of the compounds. Molecular docking studies followed by MD simulation studies (total of 500 ns) in combination with free energy calculations grade the ligands in terms of their binding affinities. In the ligand bound state of the CS, MD simulations revealed a change from stretched to bended motional shift in loop L19. The RMSF analysis also revealed this flexibility, which was confirmed by visual inspection of L19 at various time intervals during the experiment. It appears that ZF1(-25.43Kcal/mol) and ZF2 (-22.04Kcal/mol) form hbonds and have a high binding energy in the active region of protein. Residues wise distribution of binding energy reveals that Arg144, Trp4, Thr6, and L19 amino acid residues are engaged in binding of CS with inhibitors. In summary, the findings suggest that compounds ZF1 and ZF2 may be more effective and selective anti-TB agents than currently available drugs. Also the role of L19, mediated by αH9 and αH5 in the retention of ligand inside the active pocket, through the formation of lid was also revealed. This knowledge will aid in the discovery of drugs that are potent CS inhibitors. More experimental research and a better understanding of the structure-activity relationship could aid in the development of possible candidates with better CS inhibition. Communicated by Ramaswamy H. Sarma
Kinematics and Stellar Disk Modeling of Lenticular Galaxies
Creators: name: Zasov, A. V.
name: Khoperskov, A. V.
name: Katkov, I. Yu.
name: Afanasiev, V. L.
name: Kaisin, S. S.
Publisher: name: arXiv
Year: 2012
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: We present the results of spectroscopic observations of three S0-Sa galaxies: NGC338, NGC 3245, and NGC 5440 at the SAO RAS 6-m BTA telescope. The radial distributions of the line-of-sight velocities and radial velocity dispersions of stars and ionized gas were obtained, and rotation curves of galaxies were computed. We construct the numerical dynamic N-body galaxy models with N > 10^6 point masses. The models include three components: a "live" bulge, a collisionless disk, dynamically evolving to the marginally stable state, and a pseudo-isothermal dark halo. The estimates of radial velocities and velocity dispersions of stars obtained from observations are compared with model estimates, projected onto the line of sight. We show that the disks of NGC 5440 and the outer regions of NGC 338 are dynamically overheated. Taking into account the previously obtained observations, we conclude that the dynamic heating of the disk is present in a large number of early-type disk galaxies, and it seems to ensue from the external effects. The estimates of the disk mass and relative mass of the dark halo are given for seven galaxies, observed at the BTA.
description: 18 pages, 6 figures, slightly shortened version
Nonoscillatory gravitational quasinormal modes and telling tails for Schwarzschild-de Sitter black holes
Creators: name: Konoplya, R. A.
name: Zhidenko, A.
Publisher: name: arXiv
Year: 2022
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: We show that the quasinormal spectrum of gravitational perturbations of Schwarzschild - de Sitter black holes contains a new branch of purely imaginary modes. These modes are not algebraically special and we showed that the sum of them form the well-known in the literature exponential asymptotic tail. When the ratio of the event horizon radius to the cosmological horizon vanishes, these quasinormal modes approach modes of empty de Sitter spacetime. Thus, the spectrum consists of the two branches: Schwarzschild branch deformed by the cosmological constant and de Sitter branch deformed by the black hole mass. While the de Sitter branch contains purely imaginary modes only, the oscillatory modes (with nonzero real part) of the Schwarzschild branch can also become purely imaginary for some values of the cosmological constant, for which they approach the algebraically special mode.
description: 8 pages, 3 figures
Deep, wide-field, global VLBI observations of the Hubble Deep Field North and Flanking Fields
Creators: name: Chi, S.
name: Barthel, P. D.
name: Garrett, M. A.
Publisher: name: arXiv
Year: 2013
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: Dust is commonly present in weakly radio emitting star-forming galaxies and this dust may obscure the signatures of accreting black holes in these objects. We aim to uncover weak active galactic nuclei, AGN, in the faint radio source population by means of deep high-resolution radio observations. VLBI observations with a world-wide array at unparallelled sensitivity are carried out to assess the nature of the faint radio source population in the Hubble Deep Field North and its flanking fields. Images of twelve compact, AGN-driven radio sources are presented. These represent roughly one quarter of the detectable faint radio source sample. Most, but not all of these low power AGN have X-ray detections. The majority of the faint radio source population must be star-forming galaxies. Faint AGN occur in a variety of (distant) host galaxies, and these are often accompanied by a dust-obscured starburst. Deep, high-resolution VLBI is a unique, powerful technique to assess the occurrence of faint AGN.
description: Astronomy and Astrophysics, in press