cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Near-term Efficient Quantum Algorithms for Entanglement Analysis
Creators: name: Chen, Ranyiliu
name: Zhao, Benchi
name: Wang, Xin
Publisher: name: arXiv
Year: 2021
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: Entanglement plays a crucial role in quantum physics and is the key resource in quantum information processing. However, entanglement detection and quantification are believed to be hard due to the operational impracticality of existing methods. This work proposes three near-term efficient algorithms exploiting the hybrid quantum-classical technique to address this difficulty. The first algorithm finds the Schmidt decomposition--a powerful tool to analyze the properties and structure of entanglement--for bipartite pure states. While the logarithm negativity can be calculated from the Schmidt decomposition, we propose the second algorithm to estimate the logarithm negativity for bipartite pure states, where the width of the parameterized quantum circuits is further reduced. Finally, we generalize our framework for mixed states, leading to our third algorithm which detects entanglement on specific families of states, and determines disdillability in general. All three algorithms share a similar framework where the optimizations are accomplished by maximizing a cost function utilizing local parameterized quantum circuits, with better hardware efficiency and practicality compared to existing methods. The experimental implementation on Quantum Leaf using the IoP CAS superconducting quantum processor exhibits the validity and practicality of our methods for analyzing and quantifying entanglement on near-term quantum devices.
description: 16 pages, 9 figures, v3 is close to the published version
Additional file 3 of High-throughput screening identifies histone deacetylase inhibitors that modulate GTF2I expression in 7q11.23 microduplication autism spectrum disorder patient-derived cortical neurons
Creators: name: Cavallo, Francesca
name: Troglio, Flavia
name: Fagà, Giovanni
name: Fancelli, Daniele
name: Shyti, Reinald
name: Trattaro, Sebastiano
name: Zanella, Matteo
name: D’Agostino, Giuseppe
name: Hughes, James M.
name: Cera, Maria Rosaria
name: Pasi, Maurizio
name: Gabriele, Michele
name: Lazzarin, Maddalena
name: Mihailovich, Marija
name: Kooy, Frank
name: Rosa, Alessandro
name: Mercurio, Ciro
name: Varasi, Mario
name: Testa, Giuseppe
Publisher: name: figshare
Year: 2020
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 3: Figure S2. Effect of HDAC inhibitors on the expression levels of WBSCR genes.
Additional file 1 of Bone mass density following developmental exposures to perfluoroalkyl substances (PFAS): a longitudinal cohort study
Creators: name: Blomberg, Annelise
name: Mortensen, Jann
name: Weihe, Pál
name: Grandjean, Philippe
Publisher: name: figshare
Year: 2022
Subjects: subject: Biochemistry
subject: Medicine
subject: Biotechnology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Ecology
subject: FOS: Biological sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: Cancer
subject: Science Policy
subject: 110309 Infectious Diseases
subject: FOS: Health sciences

description: Additional file 1: Table S1. Count of Missing Covariates. Table S2. Baseline covariates for mother-child pairs in the Faroe Island Cohort 5, stratified by whether or not the child completed a DXA scan at age 9. Table S3. Baseline covariates of study participants, stratified by sex. Table S4. Baseline covariates of study participants, stratified by the time point of PFAS exposure measurement. Table S5. PFAS concentrations (ng/ml) by visit. Table S6. PFAS concentrations at birth (ng/ml) by study covariates. Table S7. Estimated total association between serum PFAS concentrations and aBMD at age 9, presented as the expected diference in aBMD for a doubling in serum PFAS. Table S8. Estimated ADE and ACME from causal mediation models. Fig. S1. Study selection flow chart. Fig. S2. Distribution of serum PFAS concentrations by visit. Fig. S3. Correlation of serum PFAS concentrations. Fig. S4. Associations between PFAS exposures measured at birth, 18 months, age 5 and age 9 and aBMD z-scores measured at age 9 by sex. Fig. S5. Direct and total associations between PFAS exposures measured at birth, 18 months, age 5, and age 9 and aBMD z-scores measured at age 9. Fig. S6. Associations between PFAS exposures measured at 18 months, and age 5 and 9 years and aBMD z-scores measured at age 9 years, with and without additional adjustment for duration of exclusive breastfeeding. Fig. S7. Comparison of associations between PFAS and age-, sex- and height-adjusted aBMD z-scores (primary outcome) vs. age- and sex-adjusted aBMD z-scores. Fig. S8. Estimated thin-plate splines for significant nonlinear PFAS terms. Fig. S9. Mediation of the association between 18-month PFNA and PFDA concentrations and aBMD z-scores by BMI measured at age 5 years, limited to the 244 study participants who have 18-month PFAS measurements, 9-year DXA scans, complete covariate information and BMI values measured at age 5 years.
Single-parameter spin-pumping in driven metallic rings with spin-orbit coupling
Creators: name: Ramos, J. P.
name: Torres, L. E. F. Foa
name: Orellana, P. A.
name: Apel, V. M.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: We consider the generation of a pure spin-current at zero bias voltage with a single time-dependent potential. To such end we study a device made of a mesoscopic ring connected to electrodes and clarify the interplay between a magnetic flux, spin-orbit coupling and non-adiabatic driving in the production of a spin and electrical current. By using Floquet theory, we show that the generated spin to charge current ratio can be controlled by tuning the spin-orbit coupling.
description: 10 pages, 3 figures
Additional file 4 of High-throughput screening identifies histone deacetylase inhibitors that modulate GTF2I expression in 7q11.23 microduplication autism spectrum disorder patient-derived cortical neurons
Creators: name: Cavallo, Francesca
name: Troglio, Flavia
name: Fagà, Giovanni
name: Fancelli, Daniele
name: Shyti, Reinald
name: Trattaro, Sebastiano
name: Zanella, Matteo
name: D’Agostino, Giuseppe
name: Hughes, James M.
name: Cera, Maria Rosaria
name: Pasi, Maurizio
name: Gabriele, Michele
name: Lazzarin, Maddalena
name: Mihailovich, Marija
name: Kooy, Frank
name: Rosa, Alessandro
name: Mercurio, Ciro
name: Varasi, Mario
name: Testa, Giuseppe
Publisher: name: figshare
Year: 2020
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 4. Supplemental figure legends and experimental procedures. Virus preparation for Sholl analysis; Neuronal infection; Image acquisition; Morphological analysis.
Collective behavior of minus-ended motors in mitotic microtubule asters gliding towards DNA
Creators: name: Athale, Chaitanya A.
name: Dinarina, Ana
name: Nedelec, Francois
name: Karsenti, Eric
Publisher: name: arXiv
Year: 2014
Subjects: subject: Subcellular Processes (q-bio.SC)
subject: FOS: Biological sciences

description: Microtubules (MTs) nucleated by centrosomes form star-shaped structures referred to as asters. Aster motility and dynamics is vital for genome stability, cell division, polarization and differentiation. Asters move either towards the cell center or away from it. Here, we focus on the centering mechanism in a membrane independent system of Xenopus cytoplasmic egg extracts. Using live microscopy and single particle tracking, we find that asters move towards chromatinized DNA structures. The velocity and directionality profiles suggest a random walk with drift directed towards DNA. We have developed a theoretical model that can explain this movement as a result of a gradient of MT length dynamics and MT gliding on immobilized dynein motors. In simulations, the antagonistic action of the motor species on the radial array of MTs leads to a tug-of-war purely due to geometric considerations and aster motility resembles a directed random-walk. Additionally our model predicts that aster velocities do not change greatly with varying initial distance from DNA. The movement of asymmetric asters becomes increasingly super-diffusive with increasing motor density, but for symmetric asters it becomes less super-diffusive. The transition of symmetric asters from superdiffusive to diffusive mobility is the result of number fluctuations in bound motors in the tug-of-war. Overall, our model is in good agreement with experimental data in Xenopus cytoplasmic extracts and predicts novel features of the collective effects of motor-MT interactions.
description: Keywords: Centrosomal aster, motility, simulation, tug-of-war, dynein, gliding, asymmetry, chromatin gradient, Xenopus egg extract
Pharmacoprint -- a combination of pharmacophore fingerprint and artificial intelligence as a tool for computer-aided drug design
Creators: name: Warszycki, Dawid
name: Struski, Łukasz
name: Śmieja, Marek
name: Kafel, Rafał
name: Kurczab, Rafał
Publisher: name: arXiv
Year: 2021
Subjects: subject: Quantitative Methods (q-bio.QM)
subject: Machine Learning (cs.LG)
subject: FOS: Biological sciences
subject: FOS: Computer and information sciences

description: Structural fingerprints and pharmacophore modeling are methodologies that have been used for at least two decades in various fields of cheminformatics: from similarity searching to machine learning (ML). Advances in silico techniques consequently led to combining both these methodologies into a new approach known as pharmacophore fingerprint. Herein, we propose a high-resolution, pharmacophore fingerprint called Pharmacoprint that encodes the presence, types, and relationships between pharmacophore features of a molecule. Pharmacoprint was evaluated in classification experiments by using ML algorithms (logistic regression, support vector machines, linear support vector machines, and neural networks) and outperformed other popular molecular fingerprints (i.e., Estate, MACCS, PubChem, Substructure, Klekotha-Roth, CDK, Extended, and GraphOnly) and ChemAxon Pharmacophoric Features fingerprint. Pharmacoprint consisted of 39973 bits; several methods were applied for dimensionality reduction, and the best algorithm not only reduced the length of bit string but also improved the efficiency of ML tests. Further optimization allowed us to define the best parameter settings for using Pharmacoprint in discrimination tests and for maximizing statistical parameters. Finally, Pharmacoprint generated for 3D structures with defined hydrogens as input data was applied to neural networks with a supervised autoencoder for selecting the most important bits and allowed to maximize Matthews Correlation Coefficient up to 0.962. The results show the potential of Pharmacoprint as a new, perspective tool for computer-aided drug design.
description: Journal of Chemical Information and Modeling (2021)
Molecular Gas Content of HI Monsters and Implications to Cold Gas Content Evolution in Galaxies
Creators: name: Lee, Cheoljong
name: Chung, Aeree
name: Yun, Min S.
name: Cybulski, Ryan
name: Narayanan, G.
name: Erickson, N.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: We present 12CO (J=1-0) observations of a sample of local galaxies (0.043e10Msun from the ALFALFA survey and 8 LSBs with a comparable M(HI) (>1.5e10Msun). Our sample selection is purely based on the amount of neutral hydrogen, thereby providing a chance to study how atomic and molecular gas relate to each other in these HI-massive systems. We have detected CO in 15 out of 20 ALFALFA selected galaxies and 4 out of 8 LSBs with molecular gas mass M(H2) of (1-11)e9Msun. Their total cold gas masses of (2-7e10Msun make them some of the most gas-massive galaxies identified to date in the Local Universe. Observed trends associated with HI, H2, and stellar properties of the HI massive galaxies and the field comparison sample are analyzed in the context of theoretical models of galaxy cold gas content and evolution, and the importance of total gas content and improved recipes for handling spatially differentiated behaviors of disk and halo gas are identified as potential areas of improvement for the modeling.
description: 18 pages, 11 figures, 2 tables; Accepted for publication in MNRAS
Additional file 1 of In vivo imaging of injured cortical axons reveals a rapid onset form of Wallerian degeneration
Creators: name: Canty, Alison Jane
name: Jackson, Johanna Sara
name: Huang, Lieven
name: Trabalza, Antonio
name: Bass, Cher
name: Little, Graham
name: Tortora, Maria
name: Khan, Shabana
name: Paola, Vincenzo De
Publisher: name: figshare
Year: 2020
Subjects: subject: Biophysics
subject: Biochemistry
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Neuroscience
subject: Physiology

description: Additional file 1. Canty et al. Additional file 1.pdf. Examples of fragmenting cortical axons. (a, b) Representative images and tracings of two short axon endings undergoing rapid onset WD (roWD) with time post-lesion and percentage of axon lost indicated. (c) Representative images and tracings of a branched, longer axon undergoing Wallerian degeneration (WD) with time post-lesion and percentage of axon lost indicated. Dotted boxes refer to the axon segments shown below. Scale bar is 20 μm in a, 25 μm in b and 32 μm in c.
Narrowband Photon Pair Source for Quantum Networks
Creators: name: Monteiro, F.
name: Martin, A.
name: Sanguinetti, B.
name: Zbinden, H.
name: Thew, R. T.
Publisher: name: arXiv
Year: 2013
Subjects: subject: Quantum Physics (quant-ph)
subject: Optics (physics.optics)
subject: FOS: Physical sciences

description: We demonstrate a compact photon pair source based on a periodically poled lithium niobate nonlinear crystal in a cavity. The cavity parameters are chosen such that the emitted photon pair modes can be matched in the region of telecom ultra dense wavelength division multiplexing (U-DWDM) channel spacings. This approach provides efficient, low-loss, mode selection that is compatible with standard telecommunication networks. Photons with a coherence time of 8.6 ns (116 MHz) are produced and their purity is demonstrated. A source brightness of 134 pairs(s.mW.MHz)$^{-1}$ is reported. The high level of purity and compatibility with standard telecom networks is of great importance for complex quantum communication networks.
FedGreen: Federated Learning with Fine-Grained Gradient Compression for Green Mobile Edge Computing
Creators: name: Li, Peichun
name: Huang, Xumin
name: Pan, Miao
name: Yu, Rong
Publisher: name: arXiv
Year: 2021
Subjects: subject: Machine Learning (cs.LG)
subject: FOS: Computer and information sciences

description: Federated learning (FL) enables devices in mobile edge computing (MEC) to collaboratively train a shared model without uploading the local data. Gradient compression may be applied to FL to alleviate the communication overheads but current FL with gradient compression still faces great challenges. To deploy green MEC, we propose FedGreen, which enhances the original FL with fine-grained gradient compression to efficiently control the total energy consumption of the devices. Specifically, we introduce the relevant operations including device-side gradient reduction and server-side element-wise aggregation to facilitate the gradient compression in FL. According to a public dataset, we investigate the contributions of the compressed local gradients with respect to different compression ratios. After that, we formulate and tackle a learning accuracy-energy efficiency tradeoff problem where the optimal compression ratio and computing frequency are derived for each device. Experiments results demonstrate that given the 80% test accuracy requirement, compared with the baseline schemes, FedGreen reduces at least 32% of the total energy consumption of the devices.
description: Accepted for publication in Globecom'21
Large tunable image-charge effects in single-molecule junctions
Creators: name: Perrin, M. L.
name: Verzijl, C. J. O.
name: Martin, C. A.
name: Shaikh, A. J.
name: Eelkema, R.
name: van Esch, J. H.
name: van Ruitenbeek, J. M.
name: Thijssen, J. M.
name: van der Zant, H. S. J.
name: Dulić, D.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: The characteristics of molecular electronic devices are critically determined by metal-organic interfaces, which influence the arrangement of the orbital levels that participate in charge transport. Studies on self-assembled monolayers (SAMs) show (molecule-dependent) level shifts as well as transport-gap renormalization, suggesting that polarization effects in the metal substrate play a key role in the level alignment with respect to the metal's Fermi energy. Here, we provide direct evidence for an electrode-induced gap renormalization in single-molecule junctions. We study charge transport in single porphyrin-type molecules using electrically gateable break junctions. In this set-up, the position of the occupied and unoccupied levels can be followed in situ and with simultaneous mechanical control. When increasing the electrode separation, we observe a substantial increase in the transport gap with level shifts as high as several hundreds of meV for displacements of a few ångstroms. Analysis of this large and tunable gap renormalization with image-charge calculations based on atomic charges obtained from density functional theory confirms and clarifies the dominant role of image-charge effects in single-molecule junctions.
Additional file 4 of In vivo imaging of injured cortical axons reveals a rapid onset form of Wallerian degeneration
Creators: name: Canty, Alison Jane
name: Jackson, Johanna Sara
name: Huang, Lieven
name: Trabalza, Antonio
name: Bass, Cher
name: Little, Graham
name: Tortora, Maria
name: Khan, Shabana
name: Paola, Vincenzo De
Publisher: name: figshare
Year: 2020
Subjects: subject: Biophysics
subject: Biochemistry
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Neuroscience
subject: Physiology

description: Additional file 4. AAD involves axoplasmic but not axolemmal fragmentation in spinal cord sensory axons after axotomy. (a) Axoplasmic fragmentation, AAD, occurs after laser-mediated lesion of ascending sensory neurons expressing a cytosolic form of GFP (white arrowhead at + 65 min, n = 9 axons, 5 mice). (b) Axons remain intact for longer in ascending Thy1-L15 sensory axons expressing a membrane-bound form of GFP (n = 9 axons, 5 mice). Note beading of axons, but no fragments for up to ~ 2 h postlesion. (c) The mean onset of sensory axon fragmentation is significantly shorter for GFP-M (cytosolic GFP) compared to L15 (membrane-targeted GFP) axons. (d) Mean distance of severed proximal and distal axon tips to the lesion site in GFP-M (cytosolic GFP, n = 9 axons, blue lines) and L15 (membrane-targeted GFP, n = 9 axons, orange lines). Scale bar 50 μm for a and b. *** p
Naturalness in low-scale SUSY models and "non-linear" MSSM
Creators: name: Antoniadis, I.
name: Babalic, E. M.
name: Ghilencea, D. M.
Publisher: name: arXiv
Year: 2014
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: In MSSM models with various boundary conditions for the soft breaking terms (m_{soft}) and for a higgs mass of 126 GeV, there is a (minimal) electroweak fine-tuning Delta\approx 800 to 1000 for the constrained MSSM and Delta\approx 500 for non-universal gaugino masses. These values, often regarded as unacceptably large, may indicate a problem of supersymmetry (SUSY) breaking, rather than of SUSY itself. A minimal modification of these models is to lower the SUSY breaking scale in the hidden sector (\sqrt f) to few TeV, which we show to restore naturalness to more acceptable levels Delta\approx 80 for the most conservative case of low tan_beta and ultraviolet boundary conditions as in the constrained MSSM. This is done without introducing additional fields in the visible sector, unlike other models that attempt to reduce Delta. In the present case Delta is reduced due to additional (effective) quartic higgs couplings proportional to the ratio m_{soft}/(\sqrt f) of the visible to the hidden sector SUSY breaking scales. These couplings are generated by the auxiliary component of the goldstino superfield. The model is discussed in the limit its sgoldstino component is integrated out so this superfield is realized non-linearly (hence the name of the model) while the other MSSM superfields are in their linear realization. By increasing the hidden sector scale \sqrt f one obtains a continuous transition for fine-tuning values, from this model to the usual (gravity mediated) MSSM-like models.
description: 20 pages, 7 figures
Additional file 2 of In vivo imaging of injured cortical axons reveals a rapid onset form of Wallerian degeneration
Creators: name: Canty, Alison Jane
name: Jackson, Johanna Sara
name: Huang, Lieven
name: Trabalza, Antonio
name: Bass, Cher
name: Little, Graham
name: Tortora, Maria
name: Khan, Shabana
name: Paola, Vincenzo De
Publisher: name: figshare
Year: 2020
Subjects: subject: Biophysics
subject: Biochemistry
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Neuroscience
subject: Physiology

description: Additional file 2. Canty et al. Additional file 2.pdf. Probing the onset mechanism of lesioned axons. Schematic depiction of ‘protective factor’ and ‘degeneration trigger factor’ regulated axon degeneration paradigms following a single or double lesion. Lightning bolt represents lesion site. Purple arrows indicate movement of protective factor out of the lesioned axon via one (single lesion) or two routes (double lesion). Red arrows indicate movement of a degeneration trigger into the lesioned axon via one (single lesion) or two routes (double lesion).
In silico evaluation of the toxicity of sennosides and their molecular antagonists in the phytocomplex
Creators: name: Pelini, Paolo
Publisher: name: Zenodo
Year: 2024

description: Sennosides are molecules belonging to hydroxyanthracene derivatives (anthraquinone glucosides)present in various botanical species, in particular Cassia Angustifolia L. used in medicines and foodsupplements, for its laxative effect.Recently, EFSA [1] published a report on the presumed genotoxicity of hydroxyanthracenederivatives (HAD) including sennosides especially if used in food supplements. In this context, newdata have been collected in this work evaluating, the In Silico study of the pharmacokinetic andtoxicological properties of Sennosides and the possible protective action of other molecules, inparticular phytosterols present in the phytocomplex of Cassia Angustifolia L., the results haveshown that sennosides have a low rate of bioaccessibility, but interact with P-gp protein andEstrogen Receptor ESR1 (responsible for breast cancer). on the other hand Cassia angustifolia L.possesses antagonist molecules of sennosides capable of inhibiting the activation and mutation ofESR1 such as Phytosterols (stigmasterol, campesterol) and other molecules with anti-proliferativeactivity such as 1-monolinolene.In this study we will focus on the inhibitory action of campesterol against ESR1 and therefore on itsindirect activity as an antagonist molecule against sennosides in Senna extracts.
Improvement upon Mahler's transference theorem
Creators: name: German, Oleg N.
name: Evdokimov, Konstantin G.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Number Theory (math.NT)
subject: FOS: Mathematics

description: In this paper we obtain new transference theorems improving some classical theorems which belong to Kurt Mahler. We formulate those theorems in terms of consecutive minima of pseudo-compound parallelepipeds.
A Continuous-time Stochastic Gradient Descent Method for Continuous Data
Creators: name: Jin, Kexin
name: Latz, Jonas
name: Liu, Chenguang
name: Schönlieb, Carola-Bibiane
Publisher: name: arXiv
Year: 2021
Subjects: subject: Machine Learning (cs.LG)
subject: Probability (math.PR)
subject: Statistics Theory (math.ST)
subject: FOS: Computer and information sciences
subject: FOS: Mathematics

description: Optimization problems with continuous data appear in, e.g., robust machine learning, functional data analysis, and variational inference. Here, the target function is given as an integral over a family of (continuously) indexed target functions - integrated with respect to a probability measure. Such problems can often be solved by stochastic optimization methods: performing optimization steps with respect to the indexed target function with randomly switched indices. In this work, we study a continuous-time variant of the stochastic gradient descent algorithm for optimization problems with continuous data. This so-called stochastic gradient process consists in a gradient flow minimizing an indexed target function that is coupled with a continuous-time index process determining the index. Index processes are, e.g., reflected diffusions, pure jump processes, or other Lévy processes on compact spaces. Thus, we study multiple sampling patterns for the continuous data space and allow for data simulated or streamed at runtime of the algorithm. We analyze the approximation properties of the stochastic gradient process and study its longtime behavior and ergodicity under constant and decreasing learning rates. We end with illustrating the applicability of the stochastic gradient process in a polynomial regression problem with noisy functional data, as well as in a physics-informed neural network.
Is Spiking Logic the Route to Memristor-Based Computers?
Creators: name: Gale, Ella
name: Costello, Ben de Lacy
name: Adamatzky, Andrew
Publisher: name: arXiv
Year: 2014
Subjects: subject: Emerging Technologies (cs.ET)
subject: Materials Science (cond-mat.mtrl-sci)
subject: Hardware Architecture (cs.AR)
subject: Neural and Evolutionary Computing (cs.NE)
subject: FOS: Computer and information sciences
subject: FOS: Physical sciences
subject: C.1.3; B.3.1
subject: 94C-06

description: Memristors have been suggested as a novel route to neuromorphic computing based on the similarity between neurons (synapses and ion pumps) and memristors. The D.C. action of the memristor is a current spike, which we think will be fruitful for building memristor computers. In this paper, we introduce 4 different logical assignations to implement sequential logic in the memristor and introduce the physical rules, summation, `bounce-back', directionality and `diminishing returns', elucidated from our investigations. We then demonstrate how memristor sequential logic works by instantiating a NOT gate, an AND gate and a Full Adder with a single memristor. The Full Adder makes use of the memristor's memory to add three binary values together and outputs the value, the carry digit and even the order they were input in.
description: Conference paper. Work also reported in US patent: `Logic device and method of performing a logical operation', patent application no. 14/089,191 (November 25, 2013)
Adiabatic limit of RKKY range function in one dimension
Creators: name: Cahaya, Adam B.
Publisher: name: arXiv
Year: 2021
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Mathematical Physics (math-ph)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: The RKKY interaction is an important theoretical model for indirect exchange interaction in magnetic multilayer. The expression for RKKY range function in three dimension and lower has been derived in the 1950s. However, the expression for one dimension is still studied in recent years, due to its strong singularity. By using an adiabatic limit of retarded Green's function form that directly related to RKKY interaction in one dimension, we decompose the singularity and recover the range function. Furthermore, we show in adiabatic limit, RKKY interaction also induces one-dimensional spin pumping and distance-dependent magnetic damping.
description: 6+ pages, 4 figures
Optimal friction matrix for underdamped Langevin sampling
Creators: name: Chak, Martin
name: Kantas, Nikolas
name: Lelièvre, Tony
name: Pavliotis, Grigorios A.
Publisher: name: arXiv
Year: 2021
Subjects: subject: Computation (stat.CO)
subject: Probability (math.PR)
subject: FOS: Computer and information sciences
subject: FOS: Mathematics
subject: 60J25, 60J60

description: A systematic procedure for optimising the friction coefficient in underdamped Langevin dynamics as a sampling tool is given by taking the gradient of the associated asymptotic variance with respect to friction. We give an expression for this gradient in terms of the solution to an appropriate Poisson equation and show that it can be approximated by short simulations of the associated first variation/tangent process under concavity assumptions on the log density. Our algorithm is applied to the estimation of posterior means in Bayesian inference problems and reduced variance is demonstrated when compared to the original underdamped and overdamped Langevin dynamics in both full and stochastic gradient cases.
description: 44 pages, 6 figures
Additional file 5 of In vivo imaging of injured cortical axons reveals a rapid onset form of Wallerian degeneration
Creators: name: Canty, Alison Jane
name: Jackson, Johanna Sara
name: Huang, Lieven
name: Trabalza, Antonio
name: Bass, Cher
name: Little, Graham
name: Tortora, Maria
name: Khan, Shabana
name: Paola, Vincenzo De
Publisher: name: figshare
Year: 2020
Subjects: subject: Biophysics
subject: Biochemistry
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Neuroscience
subject: Physiology

description: Additional file 5. Axon degeneration modalities. Schematic depicts the characteristics of axon degeneration for acute axonal degeneration in the spinal cord (AAD, green), rapid onset Wallerian degeneration in the cortex (roWD, blue) and Wallerian degeneration (WD) in the cortex (grey) and spinal cord (pink). From top to bottom, illustrated degeneration characteristics include the site of injury along the axon, the length of disconnected axon, the onset time at which fragmentation commences, and the fragmentation rate.
Thermalization of Nuclear Matter in Heavy-Ion Collisions at Fermi-Energies
Creators: name: Onyango, Thomas
name: Bonasera, Aldo
name: Rapp, Ralf
Publisher: name: arXiv
Year: 2021
Subjects: subject: Nuclear Theory (nucl-th)
subject: FOS: Physical sciences

description: We analyze the time evolution of the kinetic properties of nuclear matter produced in heavy-ion collisions at Fermi energies. The collision system is simulated using Constrained Molecular Dynamics (CoMD) transport calculations whose output is the isospin, position, and momentum of the nucleons. Focusing on central 35$\,$A$\cdot$MeV $^{40}$Ca+$^{40}$Ca collisions we utilize this information to extract localized momentum distributions in volume elements of 8$\,$fm$^3$ and time steps of 5$\,$fm/$c$. We then parameterize the single-particle momentum distributions with thermally motivated fit functions in the local rest frame of each cell. While the transverse-momentum distributions are well reproduced by thermal ones, the longitudinal ones carry a marked imprint of the initial nuclear motion which we capture by introducing a centroid motion into our fit functions. In particular, we find that Fermi distributions yield significantly better fits than Boltzmann ones, a consequence of the Pauli blocking implemented in CoMD. From the fits we extract the time dependence of the thermodynamic and collective properties of the excited nuclear medium. We find that the transverse temperature gradually rises to about 6$\,$MeV, which is accompanied by a dissipation of the initial centroid motion of the incoming nuclei which vanishes at about 100$\,$fm/$c$ after initial impact. We are therefore able to track the transition of beam energy into random kinetic energy for nucleons, suggesting a three-dimensional equilibration of energy in the late stages of the collision.
description: 14 pages, 11 figures
Additional file 1 of Increasing incidence of anaphylaxis in Hong Kong from 2009 to 2019—discrepancies of anaphylaxis care between adult and paediatric patients
Creators: name: Li, Philip Hei
name: Leung, Agnes S. Y.
name: Li, Rebecca M. Y.
name: Ting-Fan Leung
name: Chak-Sing Lau
name: Wong, Gary W. K.
Publisher: name: figshare
Year: 2020
Subjects: subject: Medicine
subject: Pharmacology
subject: Biotechnology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Immunology
subject: FOS: Clinical medicine
subject: Cancer
subject: Science Policy
subject: 111714 Mental Health
subject: FOS: Health sciences

description: Additional file 1: Table S1. Coding accuracy from 2009-2019 in the subgroup analysis of NTEC paediatric anaphylaxis cases. Figure S1. Incidence rates of anaphylaxis and incidence rates of newly diagnosed food allergy from 2009-2019 in the NTEC paediatric subgroup analysis. Table S2. Estimated incidence rate and incidence rate ratios of anaphylaxis from 2015-2019, using year 2014 as reference. Figure S2. Breakdown of food allergy triggers from 2009-2019 in the NTEC paediatric subgroup analysis.
Energy transport via multiphonon processes in graphene
Creators: name: Virtanen, Pauli
Publisher: name: arXiv
Year: 2013
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: The Dirac dispersion of graphene limits the phase space available for energy transport between electrons and acoustic phonons at temperatures above the Bloch-Grueneisen temperature. Consequently, energy transport can be dominated by supercollision events, involving also other scattering processes. Scattering from flexural phonons can compensate for the large momentum transfer involved in scattering from thermal acoustic phonons, and enables similar supercollision events as disorder. Such multiphonon processes are also allowed by selection rules. I show that acoustic-flexural process can in the energy transport be of the same order of magnitude as direct flexural and acoustic phonon processes, depending on electronic screening and mechanical strain.
description: 5 pages, 3 figures
Additional file 1 of Effect of 24/7 attending coverage in the neonatal intensive care unit on fellow education
Creators: name: Sahni, Mitali
name: Mowes, Anja
Publisher: name: figshare
Year: 2020
Subjects: subject: Medicine
subject: Pharmacology
subject: Biotechnology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Science Policy
subject: 110309 Infectious Diseases
subject: FOS: Health sciences

description: Additional file 1.
Phylogenetic Analysis of Cancer Evolution in Malignant Pleural Mesothelioma to Identify Driver Genes
Creators: name: Brannan, Lee D.
Publisher: name: University of Leicester
Year: 2023
Subjects: Uncategorized

description: Malignant Pleural Mesothelioma (MPM) is a rare type of cancer which occurs in the mesothelium of the lungs, and is characterised by a long latency period followed by a highly aggressive phase once fully developed. The initial tumour is the result of exposure to asbestos, and the prognosis is very poor once diagnosis has taken place. Currently, several genes have been associated with MPM, but no drivers have been identified via phylogenetic analysis. In order to identify potential driver genes which cause the cancer to mutate into its aggressive state, three distinct phylogenetic pipelines were established to process whole-exome sequencing data taken from 25 MPM patients from the MEDUSA cohort. The first pipeline used copy number calls generated from the patient cohort and incorporated them into a phylogenetic inference software in order to generate trees displaying the evolution of the cancer across 4-5 samples per patient. The second pipeline used single-nucleotide variations generated from the patient cohort and incoporated them into a second phylogenetic inference software to generate a different set of trees. The third pipeline used the output from the first in order to generate a third set of trees and establish an order of mutation for events found in the truncal regions of the first tree set. Each pipeline provided strong evidence for the Neurofibromin 2/Merlin (NF2) gene as a potential driver in the progression of the cancer from its latent state. This phylogenetic inference is among the first times such a method has been used for MPM, with the findings possibly revealing candidates for potential drug-targeting in the cancer.
Generalized Coverage Criteria for Combinatorial Sequence Testing
Creators: name: Elyasaf, Achiya
name: Farchi, Eitan
name: Margalit, Oded
name: Weiss, Gera
name: Weiss, Yeshayahu
Publisher: name: arXiv
Year: 2022
Subjects: subject: Software Engineering (cs.SE)
subject: FOS: Computer and information sciences

description: We present a new model-based approach for testing systems that use sequences of actions and assertions as test vectors. Our solution includes a method for quantifying testing quality, a tool for generating high-quality test suites based on the coverage criteria we propose, and a framework for assessing risks. For testing quality, we propose a method that specifies generalized coverage criteria over sequences of actions, which extends previous approaches. Our publicly available tool demonstrates how to extract effective test suites from test plans based on these criteria. We also present a Bayesian approach for measuring the probabilities of bugs or risks, and show how this quantification can help achieve an informed balance between exploitation and exploration in testing. Finally, we provide an empirical evaluation demonstrating the effectiveness of our tool in finding bugs, assessing risks, and achieving coverage.
description: 12 pages, 5 tables, 5 figures, and 2 listing
Additional file 1 of Respiratory health among adolescents living in the Highveld Air Pollution Priority Area in South Africa
Creators: name: Millar, Danielle A.
name: Kapwata, Thandi
name: Kunene, Zamantimande
name: Mogotsi, Mirriam
name: Wernecke, Bianca
name: Garland, Rebecca M.
name: Mathee, Angela
name: Theron, Linda
name: Levine, Diane T.
name: Ungar, Michael
name: Batini, Chiara
name: John, Catherine
name: Wright, Caradee Y.
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Biotechnology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Science Policy

description: Additional file 1.
Additional file 2 of Physiologic responses to a staircase lung volume optimization maneuver in pediatric high-frequency oscillatory ventilation
Creators: name: Jager, Pauline De
name: Burgerhof, Johannes G. M.
name: Koopman, Alette A.
name: Markhorst, Dick G.
name: Kneyber, Martin C. J.
Publisher: name: figshare
Year: 2020
Subjects: subject: Biophysics
subject: Space Science
subject: Medicine
subject: Cell Biology
subject: Physiology
subject: FOS: Biological sciences
subject: Biotechnology
subject: 69999 Biological Sciences not elsewhere classified
subject: Cancer

description: Additional file 2: Figure S1. Pooled changes in respiratory inductance plethysmography (RIP) measured during the lung volume optimization maneuver for a given continuous distending pressure (CDP) (normalized from 0 to 100%).
Interplay of electron and phonon channels in the refrigeration through molecular junctions
Creators: name: Tabatabaei, Fatemeh
name: Merabia, Samy
name: Gotsmann, Bernd
name: Prunnila, Mika
name: Niehaus, Thomas A.
Publisher: name: arXiv
Year: 2022
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: Due to their structured density of states, molecular junctions provide rich resources to filter and control the flow of electrons and phonons. Here we compute the out of equilibrium current-voltage characteristics and dissipated heat of some recently synthesized oligophenylenes (OPE3) using the Density Functional based Tight-Binding (DFTB) method within Non-Equilibrium Green's Function Theory (NEGF). We analyze the Peltier cooling power for these molecular junctions as function of a bias voltage and investigate the parameters that lead to optimal cooling performance. In order to quantify the attainable temperature reduction, an electro-thermal circuit model is presented, in which the key electronic and thermal transport parameters enter. Overall, our results demonstrate that the studied OPE3 devices are compatible with temperature reductions of several K. Based on the results, some strategies to enable high performance devices for cooling applications are briefly discussed.
Photoelastic coupling in gallium arsenide optomechanical disk resonators
Creators: name: Baker, Christopher
name: Hease, William
name: Nguyen, Dac-Trung
name: Andronico, Alessio
name: Ducci, Sara
name: Leo, Giuseppe
name: Favero, Ivan
Publisher: name: arXiv
Year: 2014
Subjects: subject: Optics (physics.optics)
subject: FOS: Physical sciences

description: We analyze the magnitude of the radiation pressure and electrostrictive stresses exerted by light confined inside GaAs semiconductor WGM optomechanical disk resonators, through analytical and numerical means, and find the electrostrictive force to be of prime importance. We investigate the geometric and photoelastic optomechanical coupling resulting respectively from the deformation of the disk boundary and from the strain-induced refractive index changes in the material, for various mechanical modes of the disks. Photoelastic optomechanical coupling is shown to be a predominant coupling mechanism for certain disk dimensions and mechanical modes, leading to total coupling g$_{om}$ and g$_0$ reaching respectively 3 THz/nm and 4 MHz. Finally, we point towards ways to maximize the photoelastic coupling in GaAs disk resonators, and we provide some upper bounds for its value in various geometries.
Linking Web Survey Tool and Data Archives
Creators: name: Brvar, Irena Vipavc
name: Vehovar, Vasja
name: Berzelak, Nejc
Publisher: name: Zenodo
Year: 2018

description: I’m sure you already heard the saying, the less work researcher will have the more likely it is survey data will actually reach data archive. At the Slovenian Social Science Data Archives (ADP), we wanted to take one step closer to researchers. We will present the work done in cooperating with the Centre of Social informatics (CSI) at the Faculty of Social Sciences, University of Ljubljana. The centre develops an open source tool for online surveys, 1KA – One click survey (www.1ka.si). As of 2018, 1KA has over 44,000 users that annually collect more than one million questionnaires. It is used by a large number of Slovenian researchers from all sectors as well as PhD students conducting online surveys for their research.

The ambition of ADP and CSI is to enable export of question level metadata, paradata, and general survey information (name, language, survey creator, field period, questionnaire duration etc.) in DDI 2.5 format that could be directly deposited in the archive. The presentation will outline the approach to developing the export of desired survey characteristics from the survey software, demonstrate its implementation and expose the key challenges related to exporting sufficiently detailed and consistent survey description in the DDI format.
The Questionnaire Design and Documentation Tool (QDDT) - a DDI based tool for assisting questionnaire design teams in their work
Creators: name: Orten, Hilde
name: Norland, Stig
name: Butt, Sarah
Publisher: name: Zenodo
Year: 2018

description: Successful large-scale international survey projects often put lots of effort into the questionnaire design and development process. The QDDT has been developed to assist the questionnaire development process by allowing questionnaire design teams to reuse metadata elements at different levels, to maintain them, to publish them and to track the development of metadata elements over time. The tool is developed and tested as part of the EU funded DASISH and SERISS projects.

The first version of this DDI based tool has just been released, and will be used in the questionnaire design process of the European Social Survey in round 10. This presentation focuses on how the workflow of questionnaire designers is supported by the DDI based design of the tool.
A 3D radiative transfer framework: XI. multi-level NLTE
Creators: name: Hauschildt, Peter H.
name: Baron, E.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: Multi-level non-local thermodynamic equilibrium (NLTE) radiation transfer calculations have become standard throughout the stellar atmospheres community and are applied to all types of stars as well as dynamical systems such as novae and supernovae. Even today spherically symmetric 1D calculations with full physics are computationally intensive. We show that full NLTE calculations can be done with fully 3 dimensional (3D) radiative transfer. With modern computational techniques and current massive parallel computational resources, full detailed solution of the multi-level NLTE problem coupled to the solution of the radiative transfer scattering problem can be solved without sacrificing the micro physics description. We extend the use of a rate operator developed to solve the coupled NLTE problem in spherically symmetric 1D systems. In order to spread memory among processors we have implemented the NLTE/3D module with a hierarchical domain decomposition method that distributes the NLTE levels, radiative rates, and rate operator data over a group of processes so that each process only holds the data for a fraction of the voxels. Each process in a group holds all the relevant data to participate in the solution of the 3DRT problem so that the 3DRT solution is parallelized within a domain decomposition group. We solve a spherically symmetric system in 3D spherical coordinates in order to directly compare our well-tested 1D code to the 3D case. We compare three levels of tests: a) a simple H+He test calculation, b) H+He+CNO+Mg, c) H+He+Fe. The last test is computationally large and shows that realistic astrophysical problems are solvable now, but they do require significant computational resources. With presently available computational resources it is possible to solve the full 3D multi-level problem with the same detailed micro-physics as included in 1D modeling.
description: 20 pages, 14 figures, A&A, in press
Combining optical spectroscopy and interferometry
Creators: name: Kraus, Stefan
Publisher: name: arXiv
Year: 2013
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: Modern optical spectrographs and optical interferometers push the limits in the spectral and spatial regime, providing important new tools for the exploration of the universe. In this contribution I outline the complementary nature of spectroscopic & interferometric observations and discuss different strategies for combining such data. Most remarkable, the latest generation of "spectro-interferometric" instruments combine the milliarcsecond angular resolution achievable with interferometry with spectral capabilities, enabling direct constraints on the distribution, density, kinematics, and ionization structure of the gas component in protoplanetary disks. I will present some selected studies from the field of star- & planet formation and hot star research in order to illustrate these fundamentally new observational opportunities.
description: Proceedings article for the "10th Potsdam Thinkshop". Accepted for publication in Astronomische Nachrichten