cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Asgard archaea modulate potential methanogenesis substrates in wetland soil
Creators: name: Valentin-Alvarado, Luis E.
name: Appler, Kathryn E.
name: Appler, Kathryn E.
name: Schölmerich, Marie
name: West-Roberts, Jacob
name: Kivenson, Veronika
name: Crits-Christoph, Alexander
name: Ly, Lynn
name: Sachdeva, Rohan
name: Savage, David F.
name: Baker, Brett J.
name: Banfield, Jillian F.
Publisher: name: ETH Zurich
Year: 2023

description: The roles of Asgard archaea in eukaryogenesis and marine biogeochemical cycles are well studied, yet their contributions in soil ecosystems are unknown. Of particular interest are Asgard archaeal contributions to methane cycling in wetland soils. To investigate this, we reconstructed two complete genomes for soil-associated Atabeyarchaeia, a new Asgard lineage, and the first complete genome of Freyarchaeia, and defined their metabolism in situ. Metatranscriptomics highlights high expression of [NiFe]-hydrogenases, pyruvate oxidation and carbon fixation via the Wood-Ljungdahl pathway genes. Also highly expressed are genes encoding enzymes for amino acid metabolism, anaerobic aldehyde oxidation, hydrogen peroxide detoxification and glycerol and carbohydrate breakdown to acetate and formate. Overall, soil-associated Asgard archaea are predicted to be non-methanogenic acetogens, likely impacting reservoirs of substrates for methane production in terrestrial ecosystems.
description: bioRxiv
Optimal control for production inventory system with various cost criterion
Creators: name: Golui, Subrata
name: Pal, Chandan
name: R., Manikandan
name: Sobhanan, Abhay
Publisher: name: arXiv
Year: 2022
Subjects: subject: Optimization and Control (math.OC)
subject: FOS: Mathematics
subject: 93E20 (Primary) 49L20, 60J27 (Secondary)

description: In this article, we investigate a dynamic control problem of a production-inventory system. Here, demands arrive at the production unit according to a Poisson process and are processed in an FCFS manner. The processing time of the customers' demand is the exponential distribution. The production manufacturers produce the items on a make-to-order basis to meet customer demands. The production is run until the inventory level becomes sufficiently large. We assume that an item's production time follows exponential distribution and the amount of time for the produced item to reach the retail shop is negligible. Also, we assume that no new customer joins the queue when there is a void inventory. This yields an explicit product-form solution for the steady-state probability vector of the system. The optimal policy that minimizes the discounted/average/pathwise average total cost per production is derived using a Markov decision process approach. We find optimal policy using value/policy iteration algorithms. Numerical examples are discussed to verify the proposed algorithms.
description: 5 figures
A Primal-Dual Approach to Solving Variational Inequalities with General Constraints
Creators: name: Chavdarova, Tatjana
name: Yang, Tong
name: Pagliardini, Matteo
name: Jordan, Michael I.
Publisher: name: arXiv
Year: 2022
Subjects: subject: Machine Learning (stat.ML)
subject: Machine Learning (cs.LG)
subject: FOS: Computer and information sciences

description: Yang et al. (2023) recently showed how to use first-order gradient methods to solve general variational inequalities (VIs) under a limiting assumption that analytic solutions of specific subproblems are available. In this paper, we circumvent this assumption via a warm-starting technique where we solve subproblems approximately and initialize variables with the approximate solution found at the previous iteration. We prove the convergence of this method and show that the gap function of the last iterate of the method decreases at a rate of $O(\frac{1}{\sqrt{K}})$ when the operator is $L$-Lipschitz and monotone. In numerical experiments, we show that this technique can converge much faster than its exact counterpart. Furthermore, for the cases when the inequality constraints are simple, we introduce an alternative variant of ACVI and establish its convergence under the same conditions. Finally, we relax the smoothness assumptions in Yang et al., yielding, to our knowledge, the first convergence result for VIs with general constraints that does not rely on the assumption that the operator is $L$-Lipschitz.
description: Source code at https://github.com/Chavdarova/I-ACVI
Complete analysis of hyperentangled Bell state in three degrees of freedom using Kerr effect and self-assisted mechanism
Creators: name: Zeng, Zhi
Publisher: name: arXiv
Year: 2022
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We present an efficient scheme for the complete hyperentangled Bell state analysis (HBSA) of photon system with polarization and two longitudinal momentum degrees of freedom (DOFs), resorting to weak cross-Kerr nonlinearity, linear optical elements and single photon detectors. In the process of distinguishing the 64 hyperentangled Bell states in three DOFs, the self-assisted mechanism is embedded, which makes our scheme simple and realizable. Moreover, we have discussed the applications of this complete HBSA scheme for high-capacity quantum communication protocols that are based on photonic hyperentanglement in three DOFs.
A deep investigation of two poorly studied open clusters Haffner 22 and Melotte 71 in Gaia era
Creators: name: Bisht, D.
name: Zhu, Quingfeng
name: Yadav, R. K. S.
name: Rangwal, Geeta
name: Sariya, Devesh P.
name: Durgapal, Alok
name: Jiang, Ing-Guey
Publisher: name: arXiv
Year: 2022
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: This paper presents a deep investigation of two open clusters, Haffner 22 and Melotte 71, using astrometric and photometric data from Gaia EDR3. We identified 382 and 597 most probable cluster members with membership probability higher than 50 percent. Mean proper motion in RA and DEC are estimated as -1.63 and 2.889 respectively for Haffner 22 and -2.398 and 4.210 for Melotte 71. A comparison of observed CMDs with theoretical isochrones leads to an age of 2.25 and 1.27 Gyr for these clusters. The distances 2.88 and 2.28 kpc based on parallax are comparable with the values derived by isochrone fitting method. Five and four blue straggler stars are identified as cluster members in Haffner 22 and Melotte 71 respectively. Based on the relative number of high velocity (binary) and single stars, we inferred binary fractions for both clusters. We found binary content is larger in core region. Mass function slope is in good agreement with the Salpeter's value while it is flat for Haffner 22. Evidence for the existence of mass segregation effect is observed in both clusters. Using the Galactic potential models, Galactic orbits are derived, indicating that both clusters follow a circular path around the Galactic center, evolving slowly.
description: This article contains 15 figures and 9 tables. This paper has been accepted for the publication in Publications of the Astronomical Society of the Pacific. arXiv admin note: text overlap with arXiv:2103.04596
Coexistance of volatile and non-volatile memristive effects in phase-separated La$_{0.5}$Ca$_{0.5}$MnO$_{3}$-based devices
Creators: name: Ramírez, G. A.
name: Acevedo, W. Román
name: Rengifo, M.
name: Nuñez, J. M.
name: Aguirre, M. H.
name: Briático, J.
name: Rubi, D.
Publisher: name: arXiv
Year: 2022
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: In this work, we have investigated the coexistance of volatile and non-volatile memristive effects in epitaxial phase-separated La$_{\text{0.5}}$Ca$_{\text{0.5}}$MnO$_{3}$ thin films. At low temperatures (50 K), we observed volatile resistive changes arising from self-heating effects in the vicinity of a metal-to-insulator transition. At higher temperatures (140 K and 200 K) we measured a combination of volatile and non-volatile effects arising from the synergy between self-heating effects and ferromagnetic-metallic phase growth induced by an external electrical field. The results reported here add phase separated manganites to the list of materials which can electrically mimic, on the same device, the behavior of both neurons and synapses, a feature that might be useful for the development of neuromorphic computing hardware
A doubly stochastic matrices-based approach to optimal qubit routing
Creators: name: Mariella, Nicola
name: Zhuk, Sergiy
Publisher: name: arXiv
Year: 2022
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: Swap mapping is a quantum compiler optimization that, by introducing SWAP gates, maps a logical quantum circuit to an equivalent physically implementable one. The physical implementability of a circuit is determined by the fulfillment of the hardware connectivity constraints. Therefore, the placement of the SWAP gates can be interpreted as a discrete optimization process. In this work, we employ a structure called doubly stochastic matrix, which is defined as a convex combination of permutation matrices. The intuition is that of making the decision process smooth. Doubly stochastic matrices are contained in the Birkhoff polytope, in which the vertices represent single permutation matrices. In essence, the algorithm uses smooth constrained optimization to slide along the edges of the polytope toward the potential solutions on the vertices. In the experiments, we show that the proposed algorithm, at the cost of additional computation time, can deliver significant depth reduction when compared to the state of the art algorithm SABRE.
A Coronal Mass Ejection and Magnetic Ejecta Observed In Situ by STEREO-A and Wind at 55$^\circ$ Angular Separation
Creators: name: Lugaz, Noé
name: Salman, Tarik M.
name: Farrugia, Charles J.
name: Yu, Wenyuan
name: Zhuang, Bin
name: Al-Haddad, Nada
name: Scolini, Camilla
name: Winslow, Réka M.
name: Möstl, Christian
name: Davies, Emma E.
name: Galvin, Antoinette B.
Publisher: name: arXiv
Year: 2022
Subjects: subject: Space Physics (physics.space-ph)
subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: We present an analysis of {\it in situ} and remote-sensing measurements of a coronal mass ejection (CME) that erupted on 2021 February 20 and impacted both the Solar TErrestrial RElations Observatory (STEREO)-A and the {\it Wind} spacecraft, which were separated longitudinally by 55$^\circ$. Measurements on 2021 February 24 at both spacecraft are consistent with the passage of a magnetic ejecta (ME), making this one of the widest reported multi-spacecraft ME detections. The CME is associated with a low-inclined and wide filament eruption from the Sun's southern hemisphere, which propagates between STEREO-A and {\it Wind} around E34. At STEREO-A, the measurements indicate the passage of a moderately fast ($\sim 425$~km\,s$^{-1}$) shock-driving ME, occurring 2--3 days after the end of a high speed stream (HSS). At {\it Wind}, the measurements show a faster ($\sim 490$~km\,s$^{-1}$) and much shorter ME, not preceded by a shock nor a sheath, and occurring inside the back portion of the HSS. The ME orientation measured at both spacecraft is consistent with a passage close to the legs of a curved flux rope. The short duration of the ME observed at {\it Wind} and the difference in the suprathermal electron pitch-angle data between the two spacecraft are the only results that do not satisfy common expectations. We discuss the consequence of these measurements on our understanding of the CME shape and extent and the lack of clear signatures of the interaction between the CME and the HSS.
description: accepted to ApJ
The Hardy inequality and large time behaviour of the heat equation on $\mathbb{R}^{N-k}\times (0,\infty)^k$
Creators: name: Cazacu, Cristian
name: Ignat, Liviu I.
name: Manea, Dragoş
Publisher: name: arXiv
Year: 2022
Subjects: subject: Analysis of PDEs (math.AP)
subject: FOS: Mathematics
subject: 35A23, 35B40, 35K67, 46E35

description: In this paper we study the large time asymptotic behaviour of the heat equation with Hardy inverse-square potential on corner spaces $\mathbb{R}^{N-k}\times (0,\infty)^k$, $k\geq 0$. We first show a new improved Hardy-Poincaré inequality for the quantum harmonic oscillator with Hardy potential. In view of that, we construct the appropriate functional setting in order to pose the Cauchy problem. Then we obtain optimal polynomial large time decay rates and subsequently the first term in the asymptotic expansion of the solutions in $L^2(\mathbb{R}^{N-k}\times (0,\infty)^k)$. Particularly, we extend and improve the results obtained by Vázquez and Zuazua (J. Funct. Anal. 2000), which correspond to the case $k=0$, to any $k\geq 0$. We emphasize that the higher the value of $k$ the better time decay rates are. We employ a different and simplified approach than Vázquez and Zuazua, managing to remove the usage of spherical harmonics decomposition in our analysis.
Characterization of Passive CMOS Strip Sensors
Creators: name: Diehl, Leena
name: Baselga, Marta
name: Gregor, Ingrid Maria
name: Hauser, Marc
name: Hemperek, Tomasz
name: Hönig, Jan Cedric
name: Jakobs, Karl
name: Mägdefessel, Sven
name: Parzefall, Ulrich
name: Rodriguez, Arturo
name: Sharma, Surabhi
name: Sperlich, Dennis
name: Wiik-Fuchs, Liv
name: Wang, Tianyang
Publisher: name: arXiv
Year: 2022
Subjects: subject: Instrumentation and Detectors (physics.ins-det)
subject: High Energy Physics - Experiment (hep-ex)
subject: FOS: Physical sciences

description: Recent advances in CMOS imaging sensor technology , e.g. in CMOS pixel sensors, have proven that the CMOS process is radiation tolerant enough to cope with certain radiation levels required for tracking layers in hadron collider experiments. With the ever-increasing area covered by silicon tracking detectors cost effective alternatives to the current silicon sensors and more integrated designs are desirable. This article describes results obtained from laboratory measurements of silicon strip sensors produced in a passive p-CMOS process. Electrical characterization and charge collection measurements with a 90Sr source and a laser with infrared wavelength showed no effect of the stitching process on the performance of the sensor.
description: 6 pages, 16 figures
Endometrial regenerative cells as a novel cell therapy attenuate experimental colitis in mice
Creators: name: Lv, Yongcheng
name: Xu, Xiaoxi
name: Zhang, Bai
name: Zhou, Guangying
name: Li, Hongyue
name: Du, Caigan
name: Han, Hongqiu
name: Wang, Hao
Publisher: name: BioMed Central
Year: 2016

description: Background: Endometrial regenerative cells (ERCs) are mesenchymal-like stem cells that can be non-invasively obtained from menstrual blood and are easily grown /generated at a large scale without tumorigenesis. We previously reported that ERCs exhibit unique immunoregulatory properties in vitro, however their immunosuppressive potential in protecting the colon from colitis has not been investigated. The present study was undertaken to determine the efficacy of ERCs in mediating immunomodulatory functions against colitis. Methods: Colitis was induced by 4% dextran-sulfate-sodium (DSS, in drinking water) in BALB/c mice for 7 days. ERCs were cultured from healthy female menstrual blood, and injected (1 million/mouse/day, i.v.) into mice on days 2, 5, and 8 following colitis induction. Colonic and splenic tissues were collected on day 14 post-DSS-induction. Clinical signs, disease activity index (DAI), pathological and immunohistological changes, cytokine profiles and cell populations were evaluated. Results: DSS-induced mice in untreated group developed severe colitis, characterized by body-weight loss, bloody stool, diarrhea, mucosal ulceration and colon shortening, as well as pathological changes of intra-colon cell infiltrations of neutrophils and Mac-1 positive cells. Notably, ERCs attenuated colitis with significantly reduced DAI, decreased levels of intra-colon IL-2 and TNF-α, but increased expressions of IL-4 and IL-10. Compared with those of untreated colitis mice, splenic dendritic cells isolated from ERC-treated mice exhibited significantly decreased MHC-II expression. ERC-treated mice also demonstrated much less CD3+CD25+ active T cell and CD3+CD8+ T cell population and significantly higher level of CD4+CD25+Foxp3+ Treg cells. Conclusions: This study demonstrated novel anti-inflammatory and immunosuppressive effects of ERCs in attenuating colitis in mice, and suggested that the unique features of ERCs make them a promising therapeutic tool for the treatment of ulcerative colitis.
Molecular formations and spectra due to electron correlations in three-electron hybrid double-well qubits
Creators: name: Yannouleas, Constantine
name: Landman, Uzi
Publisher: name: arXiv
Year: 2022
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Nuclear Theory (nucl-th)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We show that systematic full configuration-interaction (FCI) calculations enable prediction of the energy spectra and the intrinsic spatial and spin structures of the many-body wave functions as a function of the detuning parameter for the case of three-electron hybrid qubits based on GaAs asymmetric double quantum dots. Specifically, in comparison with the case of weak interactions and treating the entire three-electron double-dot hybrid qubit as an integral unit, it is shown that the predicted spectroscopic patterns, originating from strong electron correlations, manifest the formation of Wigner molecules (WMs). Signatures of WM formation include: (1) a strong suppression of the energy gaps relative to the non-interacting-electrons modeling, and (2) the appearance of a pair of avoided crossings arising between states associated with two-electron occupancies in the left and right wells. The Wigner molecule is a physical entity associated with electron localization within each well and it cannot be captured by the previously employed independent-particle or two-site-Hubbard theoretical modeling of the hybrid qubits. The emergence of strong WMs is investigated in depth through the concerted use of FCI-adapted diagnostic tools like charge and spin densities, as well as conditional probability distributions. Furthermore, the energy spectrum as a function of the strength of the Coulomb repulsion (at constant detuning) is calculated in order to complement the thorough analysis of the factors contributing to WM emergence. We report remarkable agreement with recent experimental measurements. The present FCI methodology for multi-well quantum dots can be straightforwardly extended to treat valleytronic two-band Si/SiGe hybrid qubits, where the central role of the WMs was confirmed recently.
description: Published version. 16 pages with 9 color figures. For related publications, see https://sites.gatech.edu/cyannouleas/about/
How does the partition of unity influence SORAS preconditioner?
Creators: name: Bonazzoli, Marcella
name: Claeys, Xavier
name: Nataf, Frédéric
name: Tournier, Pierre-Henri
Publisher: name: arXiv
Year: 2022
Subjects: subject: Numerical Analysis (math.NA)
subject: FOS: Mathematics

description: We investigate the influence of the choice of the partition of unity on the convergence of the Symmetrized Optimized Restricted Additive Schwarz (SORAS) preconditioner for the reaction-convection-diffusion equation. We focus on two kinds of partitions of unity, and study the dependence on the overlap and on the number of subdomains. In particular, the second kind of partition of unity, which is non-zero in the interior of the whole overlapping region, gives more favorable convergence properties, especially when increasing the overlap width, in comparison with the first kind of partition of unity, whose gradient is zero on the subdomain interfaces and which would be the natural choice for ORAS solver instead.
Bythinella corrosa Glöer & Hirschfelder, 2020, n. sp.
Creators: name: Glöer, Peter
name: Hirschfelder, Hans-Jürgen
Publisher: name: Zenodo
Year: 2020
Subjects: Biodiversity
Taxonomy
Animalia
Mollusca
Gastropoda
Littorinimorpha
Bythinellidae
Bythinella
Bythinella corrosa

description: Bythinella corrosa n. sp. [fig. 4]
 Type locality: Greece, Arcadia, Astros, spring 2.7 km south of Astros, below the main road to Leonidio on the bank of Limni Moustou, N 37°23'06.2'' / E 22°44'36.5'', 1 m a.s.l., 01.05.2017, leg. Hans-Jürgen & Andrea Hirschfelder.
 Type Material: Holotype (ZMH 140692): Shell height 2.6 mm, shell width 1.5 mm. Paratypes from type locality: ZMH (140693/2), coll. Hirschfelder (5 adult, 23 subadult).
 Etymology: The new species is named after the always corroded shell.
 Description:
 Shell: The shell is conical with the uppermost part of the embryonic whorl erected and detached. In some specimens two or more whorls are detached with a corkscrew-like appearance. The first whorls are more or less strongly corroded. The aperture is ovate, with a sharp peristome. The umbilicus is closed. The shell is 1.8-2.6 mm high and 1.3-1.5 mm broad and has about 3-3.5 whorls.
 Differentiating characters: No other Greek species shows an erected apex and partly detached whorls. B. beckmanni with the same size is much more slender and cylindrical.
 Distribution: Only known from type locality at the shore of Limni Moustou.
 Remarks: All specimens are strongly corroded and more or less deformed. Out of more than 30 investigated specimens no one showed a “normal” shape. The reason is unknown and could be due to parasitism or chemical influences. This species is the only one in Greece that lives at sea level.
description: Published as part of Glöer, Peter & Hirschfelder, Hans-Jürgen, 2020, Some new Bythinella spp. from southern Greece (Gastropoda: Bythinellidae), pp. 60-67 in Ecologica Montenegrina 30 on page 66, DOI: 10.37828/em.2020.30.5, http://zenodo.org/record/13231395
Quantum Collapse of a Thin Shell Revisited
Creators: name: Vaz, Cenalo
Publisher: name: arXiv
Year: 2022
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: There are several possible choices of the time parameter for the canonical description of a self-gravitating thin shell, but quantum thories built on different time parameters lead to unitarily inequivalent descriptions. We compare the quantum collapse of a thin dust shell in two different times {\it viz.,} the time coordinate in the interior of the shell (originally addressed in \cite{hajicek92a}) and the time coordinate of the comoving observer (proper time). In each case, we obtain exact solutions to the Wheeler-DeWitt equation requiring only a finite and well behaved $U(1)$ current. The two quantum theories are complementary and each highlights the role played by the Planck mass: stationary states of positive energy in interior time exist only if the shell rest mass in smaller than the Planck mass. In proper time they exist only when the shell rest mass is {\it greater} than the Planck mass. In coordinate time there are both scattering states and bound states with a well defined energy spectrum. In the proper time description there are only bound states, whose spectrum we determine.
description: 14 pages, no figures. To appear in Phys. Rev. D
Transcoding Unicode Characters with AVX-512 Instructions
Creators: name: Clausecker, Robert
name: Lemire, Daniel
Publisher: name: arXiv
Year: 2022
Subjects: subject: Data Structures and Algorithms (cs.DS)
subject: FOS: Computer and information sciences

description: Intel includes in its recent processors a powerful set of instructions capable of processing 512-bit registers with a single instruction (AVX-512). Some of these instructions have no equivalent in earlier instruction sets. We leverage these instructions to efficiently transcode strings between the most common formats: UTF-8 and UTF-16. With our novel algorithms, we are often twice as fast as the previous best solutions. For example, we transcode Chinese text from UTF-8 to UTF-16 at more than 5 GiB/s using fewer than 2 CPU instructions per character. To ensure reproducibility, we make our software freely available as an open source library. Our library is part of the popular Node.js JavaScript runtime.
Short-term diesel exhaust inhalation in a controlled human crossover study is associated with changes in DNA methylation of circulating mononuclear cells in asthmatics
Creators: name: Jiang, Ruiwei
name: Jones, Meaghan J.
name: Sava, Francesco
name: Kobor, Michael S. (Geneticist)
name: Carlsten, Christopher Russell
Publisher: name: BioMed Central
Year: 2015

description: Background: Changes in DNA methylation have been associated with traffic-related air pollution in observational studies, but the specific mechanisms and temporal dynamics therein have not been explored in a controlled study of asthmatics. In this study, we investigate short-term effects of diesel exhaust inhalation on DNA methylation levels at CpG sites across the genome in circulating blood in asthmatics. Methods A double-blind crossover study of filtered air and diesel exhaust exposures was performed on sixteen non-smoking asthmatic subjects. Blood samples were collected pre-exposure, and then 6 and 30 hours post-exposure. Peripheral blood mononuclear cell DNA methylation was interrogated using the Illumina Infinium HumanMethylation450 Array. Exposure-related changes in DNA methylation were identified. In addition, CpG sites overlapping with Alu or LINE1 repetitive elements and candidate microRNA loci were also analyzed. Results DNA methylation at 2827 CpG sites were affected by exposure to diesel exhaust but not filtered air; these sites enriched for genes involved in protein kinase and NFkB pathways. CpG sites with significant changes in response to diesel exhaust exposure primarily became less methylated, with a site residing within GSTP1 being among the significant hits. Diesel exhaust-associated change was also found for CpG sites overlapping with Alu and LINE1 elements as well as for a site within miR-21. Conclusion Short-term exposure to diesel exhaust resulted in DNA methylation changes at CpG sites residing in genes involved in inflammation and oxidative stress response, repetitive elements, and microRNA. This provides plausibility for the role of DNA methylation in pathways by which airborne particulate matter impacts gene expression and offers support for including DNA methylation analysis in future efforts to understand the interactions between environmental exposures and biological systems.
Revealing directed effective connectivity of cortical neuronal networks from measurements
Creators: name: Sun, Chumin
name: Lin, K. C.
name: Yeung, C. Y.
name: Ching, Emily S. C.
name: Huang, Yu-Ting
name: Lai, Pik-Yin
name: Chan, C. K.
Publisher: name: arXiv
Year: 2022
Subjects: subject: Neurons and Cognition (q-bio.NC)
subject: Biological Physics (physics.bio-ph)
subject: FOS: Biological sciences
subject: FOS: Physical sciences

description: In the study of biological networks, one of the major challenges is to understand the relationships between network structure and dynamics. In this paper, we model in vitro cortical neuronal cultures as stochastic dynamical systems and apply a method that reconstructs directed networks from dynamics [Ching and Tam, Phys. Rev. E 95, 010301(R), 2017] to reveal directed effective connectivity, namely the directed links and synaptic weights, of the neuronal cultures from voltage measurements recorded by a multielectrode array. The effective connectivity so obtained reproduces several features of cortical regions in rats and monkeys and has similar network properties as the synaptic network of the nematode C. elegans, the only organism whose entire nervous system has been mapped out as of today. The distribution of the incoming degree is bimodal and the distributions of the average incoming and outgoing synaptic strength are non-Gaussian with long tails. The effective connectivity captures different information from the commonly studied functional connectivity, estimated using statistical correlation between spiking activities. The average synaptic strengths of excitatory incoming and outgoing links are found to increase with the spiking activity in the estimated effective connectivity but not in the functional connectivity estimated using the same sets of voltage measurements. These results thus demonstrate that the reconstructed effective connectivity can capture the general properties of synaptic connections and better reveal relationships between network structure and dynamics.
Melting of magnetic order in ${\mathrm{NaOsO}}_{3}$ by fs laser pulses
Creators: name: Giorgianni, Flavio
name: Burian, Max
name: Gurung, Namrata
name: Kubli, Martin
name: Esposito, Vincent
name: Staub, Urs
name: Beaud, Paul
name: Johnson, Steven Lee
name: Windsor, Yoav William
name: Rettig, Laurenz
name: Ozerov, Dmitry
name: Lemke, Henrik
name: Saha, Susmita
name: Pressacco, Federico
name: Collins, Stephen Patrick
name: Togashi, Tadashi
name: Katayama, Tetsuo
name: Owada, Shigeki
name: Yabashi, Makina
name: Yamaura, Kazunari
name: Tanaka, Yoshikazu
name: Scagnoli, Valerio
Publisher: name: arXiv
Year: 2022
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: NaOsO$_3$ has recently attracted significant attention for the strong coupling between its electronic band structure and magnetic ordering. Here, we used time-resolved magnetic X-ray diffraction to determine the timescale of the photoinduced \afm dynamics in NaOsO$_3$. Our measurements are consistent with a sub-100~fs melting of the \afm long-range order, that occurs significantly faster than the lattice dynamics as monitored by the transient change in intensity of selected Bragg structural reflections, which instead show a decrease of intensity on a timescale of several ps.
description: 11 pages, 6 figures
The FAST Ultra-Deep Survey (FUDS): observational strategy, calibration and data reduction
Creators: name: Xi, Hongwei
name: Peng, Bo
name: Staveley-Smith, Lister
name: For, Bi-Qing
name: Liu, Bin
Publisher: name: arXiv
Year: 2022
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: The FAST Ultra-Deep Survey (FUDS) is a blind survey that aims for the direct detection of HI in galaxies at redshifts $z<0.42$. The survey uses the multibeam receiver on the Five Hundred Meter Aperture Spherical Telescope (FAST) to map six regions, each of size 0.72 deg$^2$ at high sensitivity ($\sim 50 μ$Jy) and high frequency resolution (23 kHz). The survey will enable studies of the evolution of galaxies and their HI content with an eventual sample size of $\sim 1000$. We present the science goals, observing strategy, the effects of radio frequency interference (RFI) at the FAST site, our mitigation strategies and the methods for calibration, data reduction and imaging as applied to initial data. The observations and reductions for the first field, FUDS0, are completed, with around 128 HI galaxies detected in a preliminary analysis. Example spectra are given in this paper, including a comparison with data from the overlapping GAL2577 field of Arecibo Ultra-Deep Survey (AUDS).
description: 17 pages, 19 figures, 6 tables, accepted for publication in PASA
A novel concept for a fully digital particle detector
Creators: name: Casse, Gianluigi
name: Massari, Nicola
name: Franksa, Matthew
name: Parmesana, Luca
Publisher: name: arXiv
Year: 2022
Subjects: subject: Instrumentation and Detectors (physics.ins-det)
subject: High Energy Physics - Experiment (hep-ex)
subject: FOS: Physical sciences

description: Silicon sensors are the most diffuse position sensitive device in particle physics 8 experiments and in countless applications in science and technology. They had a spectacular progress in performance over almost 40 years since their first introduction, but their evolution is now slowing down. The position resolution for single particle hits is larger than a few microns in the most advanced sensors. This value was reached already over 30 years ago [1]. The minimum ionising path length a sensor can detect is several tens of microns. There are fundamental reasons why these limits will not be substantially improved by further refinements of the current technology. This makes silicon sensors unsuitable to applications where the physics signature is the short path of a recoiling atom and constrains the layout of physics experiments where they represent by far the best option like high energy physics collider experiments. In perspective, the availability of sensors with sub-micron spatial resolution, in the order of a few tens of nanometres, would be a disruptive change for the sensor technology with a foreseeable huge impact on experiment layout and various applications of these devices. For providing such a leap in resolution, we propose a novel design based on a purely digital circuit. This disruptive concept potentially enables pixel sizes much smaller than 1μm2 and a number of advantages in terms of power consumption, readout speed and reduced thickness (for low mass sensors).
description: 12 pages, 12 figures, 10 references
Aging or DEAD: origin of the non-monotonic response to weak self-propulsion in active glasses
Creators: name: Klongvessa, Natsuda
name: Ybert, Christophe
name: Cottin-Bizonne, Cécile
name: Kawasaki, Takeshi
name: Leocmach, Mathieu
Publisher: name: arXiv
Year: 2022
Subjects: subject: Soft Condensed Matter (cond-mat.soft)
subject: Disordered Systems and Neural Networks (cond-mat.dis-nn)
subject: FOS: Physical sciences

description: Among amorphous states, glass is defined by relaxation times longer than the observation time. This nonergodic nature makes the understanding of glassy systems an involved topic, with complex aging effects or responses to further out-of-equilibrium external drivings. In this respect active glasses made of self-propelled particles have recently emerged as stimulating systems which broadens and challenges our current understanding of glasses by considering novel internal out-of-equilibrium degrees of freedom. In previous experimental studies we have shown that in the ergodicity broken phase, the dynamics of dense passive particles first slows down as particles are made slightly active, before speeding up at larger activity. Here, we show that this nonmonotonic behavior also emerges in simulations of soft active Brownian particles and explore its cause. We refute that the Deadlock by Emergence of Active Directionality (DEAD) model we proposed earlier describes our data. However, we demonstrate that the nonmonotonic response is due to activity enhanced aging, and thus confirm the link with ergodicity breaking. Beyond self-propelled systems, our results suggest that aging in active glasses is not fully understood.
All Real Projective Measurements Can be Self-tested
Creators: name: Chen, Ranyiliu
name: Mančinska, Laura
name: Volčič, Jurij
Publisher: name: arXiv
Year: 2023
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: Self-testing is the strongest form of quantum functionality verification which allows a classical user to deduce the quantum state and measurements used to produce measurement statistics. While self-testing of quantum states is well-understood, self-testing of measurements, especially in high dimensions, has remained more elusive. We demonstrate the first general result in this direction by showing that every real projective measurement can be self-tested. The standard definition of self-testing only allows for the certification of real measurements. Therefore, our work effectively broadens the scope of self-testable projective measurements to their full potential. To reach this result, we employ the idea that existing self-tests can be extended to verify additional untrusted measurements. This is known as `post-hoc self-testing'. We formalize the method of post-hoc self-testing and establish a sufficient condition for its application. Using this condition we construct self-tests for all real projective measurements. Inspired by our construction, we develop a new technique of iterative self-testing, which involves using post-hoc self-testing in a sequential manner. Starting from any established self-test, we fully characterize the set of measurements that can be verified via iterative self-testing. This provides a clear methodology for constructing new self-tests from pre-existing ones.
description: 25 pages, 2 figures. Authors in alphabetical order. More comprehensive abstract and introduction. Minor typos fixed
title: Impact of weather conditions on public transport ridership
Creators: name: Baliová, Petra
Year: 2024

description: Diese Masterarbeit erforscht die Nutzungs- und Fahrgastzahlmuster des öffentlichen Personenverkehrs in Bratislava mit Fokus auf den Zusammenhang zwischen Wetterbedingungen und Fahrgastzahlen bei Bussen, Oberleitungsbussen und Straßenbahnen. Die Methode basiert auf dem CRISP-DM Modell. Die Modellierung beinhaltet ein SARIMAX-Training für Zeitreihen sowie XGBOOST für prädiktive Analyse (predictive analysis). Die Ergebnisse zeigen, dass die Temperatur einen leichten positiven Effekt auf die Busnutzung an Wochenenden hat. Auswirkungen von Niederschlag sind dagegen signifikant negativ bei Bussen mit und ohne Oberleitung. Luftfeuchtigkeit führt zu kaum Unterschieden bei der Busnutzung, allerdings zu starken Effekten bei der Nutzung von Oberleitungsbussen an Wochenenden. Die Straßenbahnnutzung zeigt sich abhängig von hohen Temperaturen und Niederschlag an Wochenenden mit verminderter Nutzung. Schulferien sowie Feiertage führen zu einem allgemeinen Rückgang bei allen öffentlichen Transportmöglichkeiten. Abschließend erschließt diese Studie Strategien für die Planung öffentlicher Verkehrssysteme mit Fokus auf der datenbasierten Entscheidungsfindung, wie z.B. Personalplanung basierend auf Zeit- und Wetter Faktoren. Im Ganzen zeigt diese Arbeit somit Abhängigkeiten der Fahrgastzahlen im öffentlichen Verkehrssystemen von Wetterbedingungen auf, aus denen Ideen für die Verbesserung des öffentlichen Personennahverkehrs in Bratislava abgeleitet werden.
description: This thesis investigates the utilisation and ridership patterns of public transport in Bratislava, with a focus on the relationship between weather conditions and passenger numbers across buses, trolleybuses, and trams. Its methodology is grounded in the CRISP-DM model. The modelling involved training SARIMAX for time series and XGBoost for predictive analysis. The results reveal that temperature has a modest impact on bus ridership on weekends, leading to a slight increase in number of passengers, while precipitation has a significant negative impact on ridership of both buses and trolleybuses. Humidity minimally affects bus usage but significantly impacts trolleybuses on weekdays. Tram ridership declines during weekends with higher temperatures and precipitation. School and public holidays also exhibit a notable decrease in ridership across all modes of transport. Lastly, the study offers actionable strategies for urban transportation planning, emphasising data-driven decision-making such as employing resource allocation based on temporal and weather-related patterns to anticipate ridership shifts. In summary, this research contributes to understanding the impact of weather conditions on public transport ridership, providing valuable insights for the enhancement of Bratislava's transit system.
The physical connection between central stellar surface density and stellar spin in SAMI and MaNGA nearby galaxies
Creators: name: Cortese, L.
name: Fraser-McKelvie, A.
name: Woo, J.
name: Catinella, B.
name: Harborne, K.
name: van de Sande, J.
name: Bland-Hawthorn, J.
name: Brough, S.
name: Bryant, J. J.
name: Croom, S.
name: Sweet, S.
Publisher: name: arXiv
Year: 2022
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: The stellar surface density within the inner 1 kpc ($Σ_{1}$) has become a popular tool for understanding the growth of galaxies and its connection with the quenching of star formation. The emerging picture suggests that building a central dense core is a necessary condition for quenching. However, it is not clear whether changes in $Σ_{1}$ trace changes in stellar kinematics and the growth of dispersion-dominated bulges. In this paper, we combine imaging from the Sloan Digital Sky Survey with stellar kinematics from the Sydney-AAO Multi-object Integral-field unit (SAMI) and Mapping Nearby Galaxies at Apache Point Observatory (MaNGA) surveys to quantify the correlation between $Σ_{1}$ and the proxy for stellar spin parameter within one effective radius ($λ_{re}$) for 1599 nearby galaxies. We show that, on the star-forming main sequence and at fixed stellar mass, changes in $Σ_{1}$ are mirrored by changes in $λ_{re}$. While forming stars, main sequence galaxies remain rotationally-dominated systems, with their $Σ_{1}$ increasing but their stellar spin staying either constant or slightly increasing. The picture changes below the main sequence, where $Σ_{1}$ and $λ_{re}$ are no longer correlated. Passive systems show a narrower range of $Σ_{1}$, but a wider range of $λ_{re}$ compared to star-forming galaxies. Our results indicate that, from a structural point of view, passive galaxies are a more heterogeneous population than star-forming systems, and may have followed a variety of evolutionary paths. This also suggests that, if dispersion-dominated bulges still grow significantly at $z\sim$0, this generally takes place during, or after, the quenching phase.
description: 12 pages, 7 figures, 1 table. MNRAS in press
A unified theory of second sound in two dimensional materials
Creators: name: Shang, Man-Yu
name: Mao, Wen-Hao
name: Yang, Nuo
name: Li, Baowen
name: Lü, Jing-Tao
Publisher: name: arXiv
Year: 2022
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: We develop a unified theory for the second sound in two dimensional materials. Previously studied drifting and driftless second sound are two limiting cases of the theory, corresponding to the drift and diffusive part of the energy flux, respectively. We find that due to the presence of quadratic flexural phonons the drifting second sound does not exist in the thermodynamic limit, while the driftless mode is less affected. This is understood as a result of infinite effective inertia of flexual phonons, due to their constant density states and divergent Bose-Einstein distribution in the long wave length limit. Consequently, the group velocity of the drifting mode is smaller than that of the driftless mode. However, upon tensile strain, the velocity of drifting mode becomes larger. Both of them increase with tensile strain due to the linearization of the flexural phonon dispersion. Our results clarify several puzzles encountered previously and pave the way for exploring wave-like heat transport beyond hydrodynamic regime.
Additional file 6 of QSAR-derived affinity fingerprints (part 1): fingerprint construction and modeling performance for similarity searching, bioactivity classification and scaffold hopping
Creators: name: Škuta, C.
name: Cortés-Ciriano, I.
name: Dehaen, W.
name: Kříž, P.
name: Westen, G. J. P. Van
name: Tetko, I. V.
name: Bender, A.
name: Svozil, D.
Publisher: name: figshare
Year: 2020
Subjects: subject: Biochemistry
subject: Pharmacology
subject: Biotechnology
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
subject: Plant Biology

description: Additional file 6. Similarity searching and biological activity classification tasks. Plots showing the performance of the QAFFP and Morgan2 fingerprints.
Concentration limit for non-local dissipative convection-diffusion kernels on the hyperbolic space
Creators: name: González, María del Mar
name: Ignat, Liviu I.
name: Manea, Dragoş
name: Moroianu, Sergiu
Publisher: name: arXiv
Year: 2023
Subjects: subject: Analysis of PDEs (math.AP)
subject: FOS: Mathematics
subject: 45K05, 45M05, 58J35

description: We study a non-local evolution equation on the hyperbolic space $\mathbb{H}^N$. We first consider a model for particle transport governed by a non-local interaction kernel defined on the tangent bundle and invariant under the geodesic flow. We study the relaxation limit of this model to a local transport problem, as the kernel gets concentrated near the origin of each tangent space. Under some regularity and integrability conditions on the kernel, we prove that the solution of the rescaled non-local problem converges to that of the local transport equation. Then, we construct a large class of interaction kernels that satisfy those conditions.
 We also consider a non-local, non-linear convection-diffusion equation on $\mathbb{H}^N$ governed by two kernels, one for each of the diffusion and convection parts, and we prove that the solution converges to the solution of a local problem as the kernels get concentrated. We prove and then use in this sense a compactness tool on manifolds inspired by the work of Bourgain-Brezis-Mironescu.
title: Search for lepton flavor violating 𝜏 decays to a lepton and an invisible boson at Belle II using machine learning methods
Creators: name: Bacher, Benjamin
Year: 2024

description: Das Standard Model der Teilchenphysik kann bestimmte Phänomene wie Lepton Flavor Violation (LFV) und Dunkle Materie nicht erklären oder verbietet diese zum Teil sogar. Deswegen tauchen immer mehr Konzepte, die über das Standard Models hinausgehen, auf und versuchen diese Phänomene zu erklären, sogenannte Neue Physik. Ein paar dieser Theorien sagen die Existenz von zusätzlichen Bosonen voraus. Nennen wir sie ? Teilchen. Obwohl es unmöglich ist, aufgrund von sehr schwacher beziehungsweise nicht vorhandener Wechselwirkung mit bekannten Teilchen diese Teilchen mit bisherigen Methoden direkt zu messen, kann man den Querschnitt des vorhergesagten Zerfalls berechnen und mit den Spuren der messbaren Teilchen vergleichen, in unserem Fall mit ?, ? und ? Leptonen. LFV für geladene Teilchen nennt man charged LFV. Diese charged LFV Zerfälle sind, wenn sie überhaupt existieren, äußerst selten und haben deshalb ein sehr kleines Signal-zu-Hintergrund Verhältnis. Unser Ziel ist die Verbesserung von statistischer Ungenauigkeit auf der Suche nach solchen Zerfällen. Der Fokus dieser Arbeit ist deshalb die Trennung von Signal (Neue Physik Interaktionen) und Hintergrund (Standard Model Interaktionen). Wir nutzen Monte Carlo generierte Datensätze und schneiden bei bestimmten Variablen rechteckige Datensätze daraus. In Kombination mit dem Boosted Decision Tree Algorithmus können wir die vielversprechensten Schnittpunkte finden und so das Signal-zu-Hintergrund Verhältnis gesammelter Datenverbessern.
description: The Standard Model of Particle Physics (SM) does not explain or even forbids concrete phenomena like Lepton Flavor Violation (LFV) and Dark Matter. Therefore, numerous New Physics(NP) concepts beyond the SM have been brought up for theoretical and experimental research. A few of those theories predict the existence of an additional boson. Let’s call it the ? particle. Though it is impossible to detect it directly with current methods, due to non-existing or very weak interactions with known particles, we can calculate the cross-section of the predicted decay and compare the traces of the detectable particles, in this case, ?, ?, and ?. LFV for charged particles is called charged LFV. Charged LFV decays are rare events if they exist in the first place thus having a small signal-to-noise ratio. So we want to focus on improving statistics in the search for such decays. The main point of this thesis is therefore the separation of signal (NP interactions) and background (SM interactions). We use Monte Carlo samples and apply rectangular cuts on a set of discriminating variables. In combination with Boosted Decision Tree training (BDT) to find the optimal cutting point we can improve the signal-to-background ratio for data.