cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Exploring pNIPAM Lyogels: Experimental Study on Swelling Equilibria in Various Organic Solvents and Mixtures, Supported by COSMO-RS Analysis
Creators: name: Eckert, Kathrin Marina
name: Müller, Simon
name: Luinstra, Gerrit A.
name: Smirnova, Irina
Publisher: name: arXiv
Year: 2024
Subjects: subject: Soft Condensed Matter (cond-mat.soft)
subject: FOS: Physical sciences

description: Stimuli-responsive lyogels are considered to be smart materials due to their capability of undergoing significant macroscopic changes in response to external triggers. Due to their versatile and unique properties, smart lyogels exhibit great potential in various applications such as drug delivery or actuation processes. While Poly-N-isopropylacrylamide (pNIPAM) is widely known as a thermo-responsive material, it also shows significant solvent-responsive swelling behavior. As polar solvents induce strong swelling due to hydrogen bonding with the amide group, nonpolar solvents lead to significant shrinkage of the lyogels. The aim of this study is to investigate and to model this behavior for future application in chemical or biochemical reactors. As a current area of research, incorporating smart hydrogel technology into (bio-)chemical reactors facilitates the development of smart reactor systems. Applying thermodynamic modelling with the gE model COSMO-RS on the monomer or oligomers of pNIPAM, the correlation between solvent-polymer interactions and the degree of swelling can be observed. pNIPAM derivatives exhibit low infinitive dilution activity coefficients (IDACs) in polar solvents with large degrees of swelling, while displaying an increase of IDACs in nonpolar solvents. Hydrogen bonds dominate the swelling behavior of lyogels not only in pure solvents but also in mixtures of solvents with varying polarity. Even in mixtures containing high amounts of nonpolar solvents, large degrees of swelling were observed due to the uptake of the polar solvent in the lyogel matrix. This effect can be observed in binary solvent mixtures but also in representative mixtures along an esterification reaction with varying carboxylic chain length of alcohol and carboxylic acids.
Weaving classical turbulence with quantum skeleton
Creators: name: Shen, Weiyu
name: Yao, Jie
name: Yang, Yue
Publisher: name: arXiv
Year: 2024
Subjects: subject: Fluid Dynamics (physics.flu-dyn)
subject: Quantum Gases (cond-mat.quant-gas)
subject: Superconductivity (cond-mat.supr-con)
subject: FOS: Physical sciences

description: Matter entanglement is a common chaotic structure in both quantum and classical systems. Turbulence can be pictured as a tangle of vortex filaments in superfluids and viscous vortices in classical fluids. However, it is hard to explain how the statistical properties of turbulence arise from elemental structures. Here we use the quantum vortex tangle as a skeleton to generate an instantaneous classical turbulent field with intertwined vortex tubes. Combining the quantum skeleton and tunable vortex thickness makes the synthetic turbulence satisfy key statistical laws and provides valuable insights for elucidating energy cascade and extreme events. By manipulating the elemental structures, we customize turbulence with desired statistical features. This bottom-up approach of "weaving" turbulence provides a testbed for analyzing and modeling turbulence.
Judith Schlehe: Die Meereskönigin des Südens, Ratu Kidul. Geisterpolitik im javanischen Alltag
Creators: name: Dahm, Bernhard
Publisher: name: ASIEN: The German Journal on Contemporary Asia
Year: 2021

description: ASIEN: The German Journal on Contemporary Asia, Nr. 72 (1999): ASIEN (Juli)
Optimizing Monotone Chance-Constrained Submodular Functions Using Evolutionary Multi-Objective Algorithms
Creators: name: Neumann, Aneta
name: Neumann, Frank
Publisher: name: arXiv
Year: 2020
Subjects: subject: Neural and Evolutionary Computing (cs.NE)
subject: Machine Learning (cs.LG)
subject: FOS: Computer and information sciences

description: Many real-world optimization problems can be stated in terms of submodular functions. Furthermore, these real-world problems often involve uncertainties which may lead to the violation of given constraints. A lot of evolutionary multi-objective algorithms following the Pareto optimization approach have recently been analyzed and applied to submodular problems with different types of constraints. We present a first runtime analysis of evolutionary multi-objective algorithms based on Pareto optimization for chance-constrained submodular functions. Here the constraint involves stochastic components and the constraint can only be violated with a small probability of alpha. We investigate the classical GSEMO algorithm for two different bi-objective formulations using tail bounds to determine the feasibility of solutions. We show that the algorithm GSEMO obtains the same worst case performance guarantees for monotone submodular functions as recently analyzed greedy algorithms for the case of uniform IID weights and uniformly distributed weights with the same dispersion when using the appropriate bi-objective formulation. As part of our investigations, we also point out situations where the use of tail bounds in the first bi-objective formulation can prevent GSEMO from obtaining good solutions in the case of uniformly distributed weights with the same dispersion if the objective function is submodular but non-monotone due to a single element impacting monotonicity. Furthermore, we investigate the behavior of the evolutionary multi-objective algorithms GSEMO, NSGA-II and SPEA2 on different submodular chance-constrained network problems. Our experimental results show that the use of evolutionary multi-objective algorithms leads to significant performance improvements compared to state-of-the-art greedy algorithms for submodular optimization.
description: To appear in the Evolutionary Computation Journal 2024
Discrete mechanics on unitary octonions
Creators: name: Grabowski, Janusz
name: Ravanpak, Zohreh
Publisher: name: arXiv
Year: 2020
Subjects: subject: Mathematical Physics (math-ph)
subject: Differential Geometry (math.DG)
subject: FOS: Physical sciences
subject: FOS: Mathematics
subject: 17B66, 17Dxx, 20N05, 22A22, 70G45, 70Hxx

description: In this article we generalize the discrete Lagrangian and Hamiltonian mechanics on Lie groups to non-associative objects generalizing Lie groups (smooth loops). This shows that the associativity assumption is not crucial for mechanics and opens new perspectives. As a working example we obtain the discrete Lagrangian and Hamiltonian mechanics on unitary octonions.
description: 19 pages
Metasurface optical characterization using quadriwave lateral shearing interferometry
Creators: name: Khadir, Samira
name: Andrén, Daniel
name: Verre, Ruggero
name: Song, Qinghua
name: Monneret, Serge
name: Genevet, Patrice
name: Käll, Mikael
name: Baffou, Guillaume
Publisher: name: arXiv
Year: 2020
Subjects: subject: Optics (physics.optics)
subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: An optical metasurface consists of a dense and usually non-uniform layer of scattering nanostructures behaving as a continuous and extremely thin optical component, with predefined phase and intensity transmission/reflection profiles. To date, various sorts of metasurfaces (metallic, dielectric, Huygens-like, Pancharatman-Berry, etc.) have been introduced to design ultrathin lenses, beam deflectors, holograms, or polarizing interfaces. Their actual efficiencies depend on the ability to predict their optical properties and to fabricate non-uniform assemblies of billions of nanoscale structures on macroscopic surfaces. To further help improve the design of metasurfaces, precise and versatile post-characterization techniques need to be developed. Today, most of the techniques used to characterize metasurfaces rely on light intensity measurements. Here, we demonstrate how quadriwave lateral shearing interferometry (QLSI), a quantitative phase microscopy technique, can easily achieve full optical characterization of metasurfaces of any kind, as it can probe the local phase imparted by a metasurface with high sensitivity and spatial resolution. As a means to illustrate the versatility of this technique, we present measurements on two types of metasurfaces, namely Pancharatnam-Berry and effective-refractive-index metasurfaces, and present results on uniform metasurfaces, metalenses and deflectors.
Towards a Probabilistic Foundation of Relativistic Quantum Theory: The One-Body Born Rule in Curved Spacetime
Creators: name: Reddiger, Maik
name: Poirier, Bill
Publisher: name: arXiv
Year: 2020
Subjects: subject: Mathematical Physics (math-ph)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences
subject: 81T20, 81T99, 81P99, 83C47, 83C40

description: In this work we establish a novel approach to the foundations of relativistic quantum theory, which is based on generalizing the quantum-mechanical Born rule for determining particle position probabilities to curved spacetime. A principal motivator for this research has been to overcome internal mathematical problems of quantum field theory (QFT) such as the `problem of infinities' (renormalization), which axiomatic approaches to QFT have shown to be not only of mathematical but also of conceptual nature. The approach presented here is probabilistic by construction, can accommodate a wide array of dynamical models, does not rely on the symmetries of Minkowski spacetime, and respects the general principle of relativity.
 In the analytical part of this work we consider the $1$-body case under the assumption of smoothness of the mathematical quantities involved. This is identified as a special case of the theory of the general-relativistic continuity equation. While related approaches to the relativistic generalization of the Born rule assume the hypersurfaces of interest to be spacelike and the spacetime to be globally hyperbolic, we employ prior contributions by C. Eckart and J. Ehlers to show that the former condition is naturally replaced by a transversality condition and that the latter one is obsolete. We discuss two distinct formulations of the $1$-body case, which, borrowing terminology from the non-relativistic analog, we term the Lagrangian and Eulerian pictures. We provide a comprehensive treatment of both. The main contribution of this work to the mathematical physics literature is the development of the Lagrangian picture. The Langrangian picture shows how one can address the `problem of time' in this approach and therefore serves as a blueprint for the generalization to many bodies and the case that the number of bodies is not conserved (example given for the latter).
description: 86 pages, 7 figures; Keywords: relativistic conservation laws, relativistic quantum mechanics, axiomatic quantum field theory, problem of time, Dirac equation, flowout, beyond the Standard Model
Are bacteria claustrophobic? The problem of micrometric spatial confinement for the culture of micro-organisms
Creators: name: Molinaro, Céline
name: Da Cunha, Violette
name: Gorlas, Aurore
name: Iv, François
name: Gallais, Laurent
name: Catchpole, Ryan
name: Forterre, Patrick
name: Baffou, Guillaume
Publisher: name: arXiv
Year: 2020
Subjects: subject: Biological Physics (physics.bio-ph)
subject: Soft Condensed Matter (cond-mat.soft)
subject: FOS: Physical sciences

description: Culturing cells confined in microscale geometries has been reported in many studies this last decade, in particular following the development of microfluidic-based applications and lab-on-a-chip devices. Such studies usually examine growth of Escherichia coli. In this article, we show that E. coli may be a poor model and that spatial confinement can severely prevent the growth of many micro-organisms. By studying different bacteria and confinement geometries, we determine that the growth inhibition observed for some bacteria results from fast dioxygen depletion, inherent to spatial confinement, and not to any depletion of nutriments. This article unravels the physical origin of confinement problems in cell culture, highlighting the importance of oxygen depletion, and paves the way for the effective culture of bacteria in confined geometries by demonstrating enhanced cell growth in confined geometries in the proximity of air bubbles.
description: 6 pages, 4 figures
Choosing points on cubic plane curves: rigidity and flexibility
Creators: name: Banerjee, Ishan
name: Chen, Weiyan
Publisher: name: arXiv
Year: 2021
Subjects: subject: Algebraic Geometry (math.AG)
subject: Geometric Topology (math.GT)
subject: FOS: Mathematics
subject: 55R10 (primary), 55R80, 14H50 (secondary)

description: Every smooth cubic plane curve has 9 flex points and 27 sextatic points. We study the following question asked by Farb: Is it true that the known algebraic structures give all the possible ways to continuously choose $n$ distinct points on every smooth cubic plane curve, for each given positive integer $n$? We give an affirmative answer to the question when $n=9$ and 18 (the smallest open cases), and a negative answer for infinitely many $n$'s.
description: 35 pages, 4 figures. An Appendix was added to the second version, recording a related result that we learned from Curtis McMullen
Tuning of Charge Order by Uniaxial Stress in a Cuprate Superconductor
Creators: name: Thomarat, Laure
name: Elson, Frank
name: Nocerino, Elisabetta
name: Das, Debarchan
name: Ivashko, Oleh
name: Bartkowiak, Marek
name: Månsson, Martin
name: Sassa, Yasmine
name: Adachi, Tadashi
name: Zimmermann, Martin v.
name: Luetkens, Hubertus
name: Chang, Johan
name: Janoschek, Marc
name: Guguchia, Zurab
name: Simutis, Gediminas
Publisher: name: arXiv
Year: 2024
Subjects: subject: Superconductivity (cond-mat.supr-con)
subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: Strongly correlated electron materials are often characterized by competition and interplay of multiple quantum states. For example, in high-temperature cuprate superconductors unconventional superconductivity, spin- and charge-density wave orders coexist. A key question is whether competing states coexist on the atomic scale or if they segregate into distinct 'islands'. Using X-ray diffraction, we investigate the competition between charge order and superconductivity in the archetypal cuprate La(2-x)BaxCuO4, around the x = 1/8-doping, where uniaxial stress restores optimal 3D superconductivity at approximately 0.06 GPa. We find that the charge order peaks and the correlation length along the stripe are strongly reduced up to the critical stress, above which they stay constant. Simultaneously, the charge order onset temperature only shows a modest decrease. Our findings suggest that optimal 3D superconductivity is not linked to the absence of charge stripes but instead requires their arrangement into smaller 'islands'. Our results provide insight into the length scales over which the interplay between superconductivity and charge order takes place.
Shear-induced memory effects in boehmite gels
Creators: name: Sudreau, Iana
name: Manneville, Sébastien
name: Servel, Marion
name: Divoux, Thibaut
Publisher: name: arXiv
Year: 2021
Subjects: subject: Soft Condensed Matter (cond-mat.soft)
subject: Materials Science (cond-mat.mtrl-sci)
subject: Applied Physics (physics.app-ph)
subject: FOS: Physical sciences

description: Colloidal gels are formed by the aggregation of Brownian particles into clusters that are, in turn, part of a space-spanning percolated network. In practice, the microstructure of colloidal gels, which dictates their mechanical properties, strongly depends on the particle concentration and on the nature of their interactions. Yet another critical control parameter is the shear history experienced by the sample, which controls the size and density of the cluster population, via particle aggregation, cluster breakup, and restructuring. Here we investigate the impact of shear history on acid-induced gels of boehmite, an aluminum oxide. We show that following a primary gelation, these gels display a dual response depending on the shear rate $\dotγ_{\rm p}$ used to rejuvenate their microstructure. We identify a critical shear rate $\dotγ_{\rm c}$, above which boehmite gels display a gel-like viscoelastic spectrum upon flow cessation, similar to that obtained following the primary gelation. However, upon flow cessation after shear rejuvenation below $\dotγ_{\rm c}$, boehmite gels display a glassy-like viscoelastic spectrum together with enhanced elastic properties. Moreover, the nonlinear rheological properties of boehmite gels also differ on both sides of $\dotγ_{\rm c}$: weak gels obtained after rejuvenation at $\dotγ_{\rm p}>\dotγ_{\rm c}$ show a yield strain that is constant, independent of $\dotγ_{\rm p}$, whereas strong gels obtained with $\dotγ_{\rm p}<\dotγ_{\rm c}$ display a yield strain that significantly increases with $\dotγ_{\rm p}$. Our results can be interpreted in light of previous literature on shear-induced anisotropy, while we rationalize the critical shear rate in terms of a dimensionless quantity, the Mason number, comparing the strength of the shear flow to the interparticle bond force.
description: 15 pages and 14 figures
Exploring the time axis within medium-modified jets
Creators: name: Apolinário, Liliana
name: Guerrero-Rodríguez, Pablo
name: Zapp, Korinna
Publisher: name: arXiv
Year: 2024
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: In this manuscript, we illustrate how to use the newly proposed $τ$ re-clustering algorithm to select jets with different degrees of quenching without biasing their initial transverse momentum spectrum. Our study is based on Z+jet simulated events using the JEWEL Monte Carlo event generator to account for jet quenching effects. We apply the $τ$ re-clustering algorithm to extract a proxy for a time axis (formation time) within the evolving medium. This information allows us to label jets according to their fragmentation pattern and select populations with enhanced sensitivity to quenching effects. Our results illustrate the potential of jets as precision tools for QGP tomography. Further, we show that the discussed method minimizes the biases stemming from $p_{T}$-, $dR$- or mass-based jet selection.
description: 13 pages. Added references and further discussion of method and results. Figure 15 corrected. Results unchanged
Designing a molecular analysis of clonality in tumours
Creators: name: Diaz-Cano, Salvador J.
Publisher: name: figshare
Year: 2012
Subjects: Molecular Biology
Medicine
Cancer

description: Clonality analysis is used to test malignant transformation and tumour progression.
X-chromosome linked clonality assays have been employed for this purpose, but are subject
to certain technical limitations. This paper reviews the issues involved and the controls that
are necessary to ensure valid interpretation of such analyses.
Decorated sheaves and morphisms in tilted hearts
Creators: name: Lin, Yinbang
name: Wang, Sz-Sheng
name: Xia, Bingyu
Publisher: name: arXiv
Year: 2021
Subjects: subject: Algebraic Geometry (math.AG)
subject: FOS: Mathematics
subject: 14D20, 14F08 (Primary) 14D22, 14D23 (Secondary)

description: We identify limit stable pairs and stable framed sheaves as epimorphisms and monomorphisms, respectively, in tilts of the standard heart, under suitable conditions. We then identify the moduli spaces with the corresponding Quot spaces, obtaining the projectivity of the Quot spaces in these cases. We also prove a formula in a motivic Hall algebra relating the Quot spaces under a tilt.
description: 15 pages
Localizing uniformly moving single-frequency sources using an inverse 2.5D approach
Creators: name: Kasess, Christian H.
name: Kreuzer, Wolfgang
name: Soni, Prateek
name: Waubke, Holger
Publisher: name: arXiv
Year: 2024
Subjects: subject: Audio and Speech Processing (eess.AS)
subject: Sound (cs.SD)
subject: FOS: Electrical engineering, electronic engineering, information engineering
subject: FOS: Computer and information sciences

description: Localizing linearly moving sound sources using microphone arrays is challenging as the transient nature of the signal leads to relatively short observation periods. Commonly, a moving focus is used and most methods operate at least partially in the time domain. In contrast, this manuscript presents an inverse source localization algorithm for uniformly moving single-frequency sources that acts entirely in the frequency domain. For this, a 2.5D approach is utilized and a transfer function between sources and a microphone grid is derived. By solving a least squares problem using the data at the microphone grid, the unknown source distribution in the moving frame can be determined. First, the time signals need to be transformed from time into frequency domain using a windowed discrete Fourier transform (DFT), which leads to spectral leakage that depends on the length of the time interval and the analysis window used. To include spectral leakage in the numerical model, the calculation of the transfer matrix is modified using the Fourier transform of the analysis window in the DFT applied to the measurements. Currently, this approach is limited to single-frequency sources as this restriction allows for simplified calculations and reduces the computational effort. The least squares problem is solved using a Tikhonov regularization and an L-curve approach. As moving sources are considered, utilizing the Doppler effect enhances the stability of the system by combining the transfer functions for multiple frequencies in the measured signals. The performance is validated using simulated data of a moving point source with or without a reflecting ground. Numerical experiments are performed to show the effect of the choice of frequencies in the receiver spectrum, the effect of the DFT, the source frequency, the distance between source and receiver, and the robustness with respect to noise.
description: 35 pages, 17 figures
Clonal patterns in phaeochromocytomas and MEN-2A adrenal medullary hyperplasias: histological and kinetic correlates
Creators: name: Diaz-Cano, Salvador J.
name: Blanes, Alfredo
name: H Galera
name: H J Wolfe
name: M De Miguel
name: R Tashjian
Publisher: name: figshare
Year: 2012
Subjects: subject: Molecular Biology
subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Cell Biology
subject: Cancer

description: The relationship among histological features, cell kinetics, and clonality has not been studied in adrenal medullary hyperplasias (AMHs) and phaeochromocytomas (PCCs). Thirty-four PCCs (23 sporadic and 11 MEN-2A (multiple endocrine neoplasia type 2A)-related tumours, the latter associated with AMH) from females were included in this study. Representative samples were histologically evaluated and microdissected to extract DNA and evaluate the methylation pattern of the androgen receptor alleles. At least two tissue samples (from the peripheral and internal zones in each tumour) were analysed with appropriate tissue controls run in every case. The same areas were selected for MIB-1 staining and in situ end labelling (ISEL). Malignant PCCs were defined by histologically confirmed distant metastases. All monoclonal AMH nodules from the same patient showed the same X-chromosome inactivated. Six sporadic PCCs revealed liver metastases (malignant PCC) and eight additional sporadic PCCs showed periadrenal infiltration (locally invasive PCC). All informative PCCs were monoclonal, except for five locally invasive PCCs and one benign PCC that revealed polyclonal patterns. Those cases also showed a fibroblastic stromal reaction with prominent blood vessels, focal smooth muscle differentiation, and significantly higher MIB-1 (126.8+/-29.9) and ISEL (50.9+/-12.8) indices. Concordant X-chromosome inactivation in nodules from a given patient suggests that MEN-2A AMH is a multifocal monoclonal condition. A subgroup of PCCs characterized by balanced methylation of androgen receptor alleles, high cellular turnover, and stromal proliferation also shows locally invasive features.
VB-structures and generalizations
Creators: name: Grabowski, Janusz
name: Grabowska, Katarzyna
name: Ravanpak, Zohreh
Publisher: name: arXiv
Year: 2021
Subjects: subject: Differential Geometry (math.DG)
subject: Mathematical Physics (math-ph)
subject: FOS: Mathematics
subject: FOS: Physical sciences
subject: 53C15, 57R22, 58A32, (Primary) 58A20, 58A30, 58D19 (Secondary)

description: Motivated by properties of higher tangent lifts of geometric structures, we introduce concepts of weighted structures for various geometric objects on a manifold F equipped with a homogeneity structure. The latter is a smooth action on F of the monoid of multiplicative reals. Vector bundles are particular cases of homogeneity structures with the action being the multiplication of vectors by reals, and weighted structures on them we call VB-structures. In the case of Lie algebroids and Lie groupoids, the weighted structures include the concepts of VB-algebroids and VB-groupoids, intensively studied recently in the literature. Investigating various weighted structures, we prove some interesting results about their properties.
description: 46 pages
E-cadherin and adenomatous polyposis coli mutations are synergistic in intestinal tumor initiation in mice
Creators: name: Diaz-Cano, Salvador J.
name: C Birchmeier
name: S Jagmohan-Changur
name: R Fodde
name: P Ruiz
name: W Birchmeier
name: C Breukel
name: A Luz
name: R Smits
Publisher: name: figshare
Year: 2012
Subjects: subject: Molecular Biology
subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Developmental Biology
subject: Cell Biology
subject: Cancer

description: Inactivation of the adenomatous polyposis coli (APC) gene is observed at early stages of intestinal tumor formation, whereas loss of E-cadherin is usually associated with tumor progression. Because both proteins compete for the binding to beta-catenin, an essential component of the Wnt signaling pathway, reduction of E-cadherin levels in an Apc mouse model could influence both tumor initiation and progression. In addition, loss or haploinsufficiency of E-cadherin may affect tumorigenesis by altering its cell-adhesive and associated functions.
 Apc1638N mice were bred with animals carrying a targeted E-cadherin knockout mutation.
 Double heterozygous animals showed a significant 9-fold and 5-fold increase of intestinal and gastric tumor numbers, respectively, compared with Apc1638N animals. The intestinal tumors of both groups showed no significant differences in grading and staging. Loss of heterozygosity analysis at the Apc and E-cadherin loci in both intestinal and gastric Apc(+/1638N)/E-cad(+/-) tumors revealed loss of the wild-type Apc allele in most cases, whereas the wild-type E-cadherin allele was always retained. This was supported by a positive, although reduced, staining for E-cadherin of intestinal tumor sections.
 Introduction of the E-cadherin mutation in Apc1638N animals enhances Apc-driven tumor initiation without clearly affecting tumor progression.
Atlas – a data warehouse for integrative bioinformatics
Creators: name: Shah, Sohrab P.
name: Huang, Yong
name: Xu, Tao
name: Yuen, Macaire M.
name: Ling, John
name: Ouellette, B. F. F.
Publisher: name: BioMed Central
Year: 2016

description: Background: We present a biological data warehouse called Atlas that locally stores and integrates biological sequences, molecular interactions, homology information, functional annotations of genes, and biological ontologies. The goal of the system is to provide data, as well as a software infrastructure for bioinformatics research and development. Description: The Atlas system is based on relational data models that we developed for each of the source data types. Data stored within these relational models are managed through Structured Query Language (SQL) calls that are implemented in a set of Application Programming Interfaces (APIs). The APIs include three languages: C++, Java, and Perl. The methods in these API libraries are used to construct a set of loader applications, which parse and load the source datasets into the Atlas database, and a set of toolbox applications which facilitate data retrieval. Atlas stores and integrates local instances of GenBank, RefSeq, UniProt, Human Protein Reference Database (HPRD), Biomolecular Interaction Network Database (BIND), Database of Interacting Proteins (DIP), Molecular Interactions Database (MINT), IntAct, NCBI Taxonomy, Gene Ontology (GO), Online Mendelian Inheritance in Man (OMIM), LocusLink, Entrez Gene and HomoloGene. The retrieval APIs and toolbox applications are critical components that offer end-users flexible, easy, integrated access to this data. We present use cases that use Atlas to integrate these sources for genome annotation, inference of molecular interactions across species, and gene-disease associations. Conclusion: The Atlas biological data warehouse serves as data infrastructure for bioinformatics research and development. It forms the backbone of the research activities in our laboratory and facilitates the integration of disparate, heterogeneous biological sources of data enabling new scientific inferences. Atlas achieves integration of diverse data sets at two levels. First, Atlas stores data of similar types using common data models, enforcing the relationships between data types. Second, integration is achieved through a combination of APIs, ontology, and tools. The Atlas software is freely available under the GNU General Public License at: http://bioinformatics.ubc.ca/atlas/
Excitability and memory in a time-delayed optoelectronic neuron
Creators: name: Martins, Jonas Mayer
name: Gurevich, Svetlana V.
name: Javaloyes, Julien
Publisher: name: arXiv
Year: 2024
Subjects: subject: Pattern Formation and Solitons (nlin.PS)
subject: Optics (physics.optics)
subject: FOS: Physical sciences

description: We study the dynamics of an optoelectronic circuit composed of an excitable nanoscale resonant-tunneling diode (RTD) driving a nanolaser diode (LD) coupled via time-delayed feedback. Using a combination of numerical path-continuation methods and time simulations, we demonstrate that this RTD-LD system can serve as an artificial neuron, generating pulses in the form of temporal localized states (TLSs) that can be employed as memory for neuromorphic computing. In particular, our findings reveal that the prototypical delayed FitzHugh-Nagumo model previously employed to model the RTD-LD resembles our more realistic model only in the limit of a slow RTD. We show that the RTD time scale plays a critical role in memory capacity as it governs a shift in pulse interaction from repulsive to attractive, leading to a transition from stable to unstable multi-pulse TLSs. Our theoretical analysis uncovers features and challenges previously unknown for the RTD-LD system, including the multistability of TLSs and attractive interaction forces, stemming from the previously neglected intrinsic dynamics of the laser. These effects are crucial to consider since they define the memory properties of the RTD-LD.
description: 17 pages, 9 figures. V2: corrected typos, clarified passages
Average-case Speedup for Product Formulas
Creators: name: Chi-Fang
name: Chen
name: Brandão, Fernando G. S. L.
Publisher: name: arXiv
Year: 2021
Subjects: subject: Quantum Physics (quant-ph)
subject: Mathematical Physics (math-ph)
subject: Functional Analysis (math.FA)
subject: Probability (math.PR)
subject: FOS: Physical sciences
subject: FOS: Mathematics

description: Quantum simulation is a promising application of future quantum computers. Product formulas, or Trotterization, are the oldest and still remain an appealing method to simulate quantum systems. For an accurate product formula approximation, the state-of-the-art gate complexity depends on the number of terms in the Hamiltonian and a local energy estimate. In this work, we give evidence that product formulas, in practice, may work much better than expected. We prove that the Trotter error exhibits a qualitatively better scaling for the vast majority of input states, while the existing estimate is for the worst states. For general $k$-local Hamiltonians and higher-order product formulas, we obtain gate count estimates for input states drawn from any orthogonal basis. The gate complexity significantly improves over the worst case for systems with large connectivity. Our typical-case results generalize to Hamiltonians with Fermionic terms, with input states drawn from a fixed-particle number subspace, and with Gaussian coefficients (e.g., the SYK models). Technically, we employ a family of simple but versatile inequalities from non-commutative martingales called $\textit{uniform smoothness}$, which leads to $\textit{Hypercontractivity}$, namely $p$-norm estimates for $k$-local operators. This delivers concentration bounds via Markov's inequality. For optimality, we give analytic and numerical examples that simultaneously match our typical-case estimates and the existing worst-case estimates. Therefore, our improvement is due to asking a qualitatively different question, and our results open doors to the study of quantum algorithms in the average case.
description: 51 pages, 10 figures; v2 improved presentation and included numerical simulation
Adaptive FRIT-based Recursive Robust Controller Design Using Forgetting Factors
Creators: name: Tsuruhara, Satoshi
name: Ito, Kazuhisa
Publisher: name: arXiv
Year: 2024
Subjects: subject: Systems and Control (eess.SY)
subject: FOS: Electrical engineering, electronic engineering, information engineering

description: Adaptive FRIT (A-FRIT) with exponential forgetting (EF) has been proposed for time-varying systems to improve the data dependence of FRIT, which is a direct data-driven tuning method. However, the EF-based method is not a reliable controller because it can cause significant degradation of the control performance and instability unless the persistent excitation (PE) condition is satisfied. To solve this problem, we propose a new A-FRIT method based on directional forgetting (DF) and exponential resetting that can forget old data without instability regardless of the PE condition. To confirm the effectiveness of the proposed method, we applied it to artificial muscle control with strong asymmetric hysteresis characteristics and evaluated its robust performance against load changes during the experiment. The experimental results show that the proposed method based on DF achieves high control performance and is robust against changes in the characteristics and/or target trajectory. The proposed method is also practical because it does not require system identification, model structure, or prior experimentation.
description: This work has been accepted to The 32nd Mediterranean Conference on Control and Automation (MED2024)
Emerging synergies in polycentric cities? Exploring the impact of intercity cooperation on labour market integration in the Yangtze River Delta, 2014–2021
Creators: name: Liu, Xueqing
name: Yang, Yuting
name: Derudder, Ben
name: Witlox, Frank
Publisher: name: Taylor & Francis
Year: 2025
Subjects: subject: Biochemistry
subject: Sociology
subject: FOS: Sociology
subject: Environmental Sciences not elsewhere classified
subject: Information Systems not elsewhere classified
subject: Science Policy
subject: Computational Biology

description: The creation of regional synergies has received much attention, both as an analytical framework and a normative goal in urban and regional development studies. One of the key mechanisms underlying synergies – cooperation – is particularly relevant for understanding how cities and their labour markets regionally integrate. Yet city cooperation remains poorly understood in conceptual and empirical terms. In addition, it is unclear to what extent intercity cooperation and the effects of the ensuing labour market integration are consistent across cities with different urban structures. Drawing on intercity patent transfer data, we explore the presence of synergies by examining cooperative relations between cities. Using a longitudinal analytical framework, we focus on China’s Yangtze River Delta megacity-region from 2014 to 2021 to explore the impact of intercity cooperation on labour market integration within polycentric urban settings. Our analysis reveals that: (1) intercity cooperation derived from technology linkages has a U-shaped effect on labour market integration and (2) polycentric structures not only contribute to this integration but also moderate the relationship between intercity cooperation and labour market dynamics. We reflect on the broader implications of our empirical findings for regional development strategies and discuss possible avenues for future research.
Internet ist ein Schrotthaufen - mit Perlen drin" - Über den Nutzen des Internets fur Südostasien-Studien
Creators: name: Wischermann, Jörg
name: Sander, Ingvar
Publisher: name: ASIEN: The German Journal on Contemporary Asia
Year: 2021

description: ASIEN: The German Journal on Contemporary Asia, Nr. 72 (1999): ASIEN (Juli)
Critical analysis of histologic criteria for grading atypical (dysplastic) melanocytic nevi
Creators: name: Diaz-Cano, Salvador J.
name: Blanes, Alfredo
name: L Pozo-Garcia
name: M Naase
name: R Cerio
Publisher: name: figshare
Year: 2012
Subjects: Medicine
Cell Biology
Cancer

description: Low concordance in grading atypical (dysplastic) melanocytic nevi (AMN) has been reported, and no systematic evaluation is available. We studied 123 AMN with architectural and cytologic atypia (40 associated with atypical-mole syndrome), classified according to standard criteria by 3 independent observers. Histologic variables included junctional and dermal symmetry, lateral extension, cohesion and migration of epidermal melanocytes, maturation, regression, nuclear features, nuclear grade, melanin, inflammatory infiltrate location, and fibroplasia. AMN (43 junctional and 80 compound) were graded mild (31), moderate (61), and severe (31). AMN-severe correlated with 3 or more nuclear abnormalities (especially pleomorphism, heterogeneous chromatin, and prominent nucleolus) and absence of regression, mixed junctional pattern, and suprabasilar melanocytes on top of lentiginous hyperplasia. AMN-severe diagnostic accuracy was 99.5% using these criteria, but only the absence of nuclear pleomorphism differentiated AMN-mild from AMN-moderate. No architectural features distinguishing AMN-mild from AMN-moderate were selected as significant by the discriminant analysis. AMN from atypical-mole syndrome revealed subtle architectural differences, but none were statistically significant in the discriminant analysis. Histologic criteria can reliably distinguish AMN-severe but fail to differentiate AMN-mild from AMN-moderate. AMN from atypical-mole syndrome cannot be diagnosed using pathologic criteria alone.
Interplay between wall slip and shear banding in a thixotropic yield stress fluid
Creators: name: Geri, Michela
name: Saint-Michel, Brice
name: Divoux, Thibaut
name: McKinley, Gareth H.
name: Manneville, Sebastien
Publisher: name: arXiv
Year: 2021
Subjects: subject: Soft Condensed Matter (cond-mat.soft)
subject: FOS: Physical sciences

description: We study the local dynamics of a thixotropic yield stress fluid that shows a pronounced non-monotonic flow curve. This mechanically unstable behavior is generally not observable from standard rheometry tests, resulting in a stress plateau that stems from the coexistence of a flowing band with an unyielded region below a critical shear rate $\dot γ_c$. Combining ultrasound velocimetry with standard rheometry, we discover an original shear-banding scenario in the decreasing branch of the flow curve of model paraffin gels, in which the flow profile of the flowing band is set by the applied shear rate $\gd$ instead of $\dot γ_c$. As a consequence, the material slips at the walls with a velocity that shows a non-trivial dependence on the applied shear rate. To capture our observations, we propose a differential version of the so-called lever rule, describing the extent of the flowing band and the evolution of wall slip with shear rate. This phenomenological model holds down to very low shear rates, at which the dimension of the flowing band becomes comparable to the size of the wax particles that constitute the gel microstructure, leading to cooperative effects. Our approach provides a framework where constraints imposed in the classical shear-banding scenario can be relaxed, with wall slip acting as an additional degree of freedom.
description: 12 pages, 9 figures
Passive decoy-state quantum secure direct communication with heralded single-photon source
Creators: name: Ying, Jia-Wei
name: Zhao, Peng
name: Zhong, Wei
name: Du, Ming-Ming
name: Li, Xi-Yun
name: Shen, Shu-Ting
name: Zhang, An-Lei
name: Zhou, Lan
name: Sheng, Yu-Bo
Publisher: name: arXiv
Year: 2024
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: Quantum secure direct communications (QSDC) can directly transmit secret messages through a quantum channel without keys. The imperfect photon source is a major obstacle for QSDC's practical implementation. The unwanted vacuum state and multiphoton components emitted from imperfect photon source largely reduce QSDC's secrecy message capacity and even threaten its security. In the paper, we propose a high-efficient passive decoy-state QSDC protocol with the heralded single-photon source (HSPS). We adopt a spontaneous parametric down-conversion source to emit entangled photon pairs in two spatial modes. By detecting the photons in one of the two correlated spatial modes, we can infer the photon-number distribution of the other spatial mode. Meanwhile, our protocol allows a simple passive preparation of the signal states and decoy state. The HSPS can effectively reduce the probability of vacuum state and increase QSDC's secrecy message capacity. Meanwhile, the passive decoy-state method can simplify the experimental operations and enhance QSDC's robustness against the third-party side-channel attacks. Under the communication distance of 10 km, the secrecy message capacity of our QSDC protocol can achieve 81.85 times with average photon number of 0.1 and 12.79 times with average photon number of 0.01 of that in the original single-photon-based QSDC protocol without the HSPS. Our QSDC protocol has longer maximal communication distance about 17.975 km with average photon number of 0.01. Our work serves as a major step toward the further development of practical passive decoy-state QSDC systems.
description: 13 pages, 5 figures
title: Journal of Computational Geometry, Vol. 14 No. 2 (2023): Special Issue of Selected Papers from SoCG 2022
title: Special Issue of Selected Papers from SoCG 2022
titleType: AlternativeTitle
Creators: name: Journal Of Computational Geometry
Publisher: name: Journal of Computational Geometry
Year: 2023

description: Special Issue of Selected Papers from the 38th International Symposium on Computational Geometry (SoCG 2022)
description: GPU computation of the Euler characteristic curve for imaging data...3–25 Hop-spanners for geometric intersection graphs...26–64 Nearly-doubling spaces of persistence diagrams...65–82 Dynamic time warping under translation: Approximation guided by space-filling curves...83–107 Minimum-error triangulations for sea surface reconstruction...108–171
Molecular and kinetic features of transitional cell carcinomas of the bladder: biological and clinical implications
Creators: name: Diaz-Cano, Salvador J.
name: Blanes, Alfredo
name: S I Baithun
name: M Naase
Publisher: name: figshare
Year: 2012
Subjects: subject: Molecular Biology
subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Cell Biology
subject: Cancer

description: Molecular and kinetic analyses have contributed to our understanding of the biology of transitional cell carcinomas (TCC) of the bladder. The concordant pattern of X-chromosome inactivation of multiple TCCs appearing at different times and at different sites and concordant genetic abnormalities in a subset of muscle-invasive TCC strongly support a monoclonal origin and a homogeneous tumor cell selection throughout the neoplasm. However, topographic intratumor heterogeneity results from the accumulation of genetic lesions in tumor suppressor genes, predominantly neurofibromatosis (NF)-1-defective in the superficial compartment and tumor protein p53 (TP53)-defective in the deep one, with lower proliferation and down-regulation of apoptosis in the latter. TCCs follow the general concept of multistep carcinogenesis and proceed through two distinct genetic pathways responsible for generating different TCC morphologies. These are the inactivation of cyclin-dependent kinase inhibitors (p15, p16, and p21WAF/CIP1) in low-grade TCC and early TP53-mediated abnormalities in high-grade TCC. TCC progression correlates with genetic instability and accumulation of collaborative genetic lesions mainly involving TP53, retinoblastoma (RB)-1, and growth factors. Distinctive genetic (low incidence of RB-1 and NF-1 abnormalities) and kinetic (slower cell turnover) profiles also correlate with a "single-file" infiltration pattern and poor survival in muscle-invasive TCCs. The underlying molecular changes of carcinoma in situ involve multiple and more extensive deletions (normally TP53-defective) than coexistent invasive TCC, suggesting an independent genetic evolution, while low-grade dysplasia is mainly polyclonal and shows a low rate of gene deletions.
Hop-Spanners for Geometric Intersection Graphs
Creators: name: Conroy, Jonathan B.
name: Tóth, Csaba D.
Publisher: name: arXiv
Year: 2021
Subjects: subject: Computational Geometry (cs.CG)
subject: Combinatorics (math.CO)
subject: FOS: Computer and information sciences
subject: FOS: Mathematics

description: A $t$-spanner of a graph $G=(V,E)$ is a subgraph $H=(V,E')$ that contains a $uv$-path of length at most $t$ for every $uv\in E$. It is known that every $n$-vertex graph admits a $(2k-1)$-spanner with $O(n^{1+1/k})$ edges for $k\geq 1$. This bound is the best possible for $1\leq k\leq 9$ and is conjectured to be optimal due to Erdős' girth conjecture.
 We study $t$-spanners for $t\in \{2,3\}$ for geometric intersection graphs in the plane. These spanners are also known as \emph{$t$-hop spanners} to emphasize the use of graph-theoretic distances (as opposed to Euclidean distances between the geometric objects or their centers). We obtain the following results: (1) Every $n$-vertex unit disk graph (UDG) admits a 2-hop spanner with $O(n)$ edges; improving upon the previous bound of $O(n\log n)$. (2) The intersection graph of $n$ axis-aligned fat rectangles admits a 2-hop spanner with $O(n\log n)$ edges, and this bound is tight up to a factor of $\log \log n$. (3) The intersection graph of $n$ fat convex bodies in the plane admits a 3-hop spanner with $O(n\log n)$ edges. (4) The intersection graph of $n$ axis-aligned rectangles admits a 3-hop spanner with $O(n\log^2 n)$ edges.
description: 36 pages, 24 figures, full version of an extended abstract in the Proceedings of SoCG 2022