cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Extensive recombination rate variation in the house mouse species complex inferred from genetic linkage maps
Creators: name: Dumont, B. L.
name: White, M. A.
name: Payseur, B. A.
name: Steffy, B.
name: Wiltshire, T.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2011

description: The rate of recombination is a key genomic parameter that displays considerable variation among taxa. Species comparisons have demonstrated that the rate of evolution in recombination rate is strongly dependent on the physical scale of measurement. Individual recombination hotspots are poorly conserved among closely related taxa, whereas genomic-scale recombination rate variation bears a strong signature of phylogenetic history. In contrast, the mode and tempo of evolution in recombination rates measured on intermediate physical scales is poorly understood. Here, we conduct a detailed statistical comparison between two whole-genome F2 genetic linkage maps constructed from experimental intercrosses between closely related house mouse subspecies (Mus musculus). Our two maps profile a common wild-derived inbred strain of M. m. domesticus crossed to distinct wild-derived inbred strains representative of two other house mouse subspecies, M. m. castaneus and M. m. musculus. We identify numerous orthologous genomic regions with significant map length differences between these two crosses. Because the genomes of these recently diverged house mice are highly collinear, observed differences in map length (centimorgans) are suggestive of variation in broadscale recombination rate (centimorgans per megabase) within M. musculus. Collectively, these divergent intervals span 19% of the house mouse genome, disproportionately aggregating on the X chromosome. In addition, we uncover strong statistical evidence for a large effect, sex-linked, site-specific modifier of recombination rate segregating within M. musculus. Our findings reveal considerable variation in the megabase-scale recombination landscape among recently diverged taxa and underscore the continued importance of genetic linkage maps in the post-genome era.
Genetic analysis of complex traits in the emerging Collaborative Cross
Creators: name: Collins, Francis S.
name: Schwartz, David A.
name: Aylor, David L.
name: Steigerwalt, Jill
name: Ferris, Martin T.
name: Chesler, Elissa J.
name: Powell, Christine L.
name: Frelinger, Jeff A.
name: Bell, Timothy A.
name: Branstetter, Lisa A.
name: Hua, Kunjie
name: Baric, Ralph S.
name: Frieman, Matt B.
name: Valdar, William
name: Foulds-Mathes, Wendy
name: Verdugo, Ricardo A.
name: Spence, Jason
name: McMillan, Leonard
name: Heise, Mark
name: Sarkar, Abhishek
name: Xie, Yuying
name: Miller, Darla R.
name: Buus, Ryan J.
name: Zhang, Qi
name: Didion, John D.
name: Yang, Ivana V.
name: Nehrenberg, Derrick L.
name: Kelada, Samir N.P.
name: Liu, Eric Yi
name: Wang, Wei
name: Gralinski, Lisa E.
name: Wang, Jeremy
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2011

description: The Collaborative Cross (CC) is a mouse recombinant inbred strain panel that is being developed as a resource for mammalian systems genetics. Here we describe an experiment that uses partially inbred CC lines to evaluate the genetic properties and utility of this emerging resource. Genome-wide analysis of the incipient strains reveals high genetic diversity, balanced allele frequencies, and dense, evenly distributed recombination sites—all ideal qualities for a systems genetics resource. We map discrete, complex, and biomolecular traits and contrast two quantitative trait locus (QTL) mapping approaches. Analysis based on inferred haplotypes improves power, reduces false discovery, and provides information to identify and prioritize candidate genes that is unique to multifounder crosses like the CC. The number of expression QTLs discovered here exceeds all previous efforts at eQTL mapping in mice, and we map local eQTL at 1-Mb resolution. We demonstrate that the genetic diversity of the CC, which derives from random mixing of eight founder strains, results in high phenotypic diversity and enhances our ability to map causative loci underlying complex disease-related traits.
Charge Regulation of Polyelectrolyte Gels: Swelling Transition
Creators: name: Zheng, Bin
name: Avni, Yael
name: Andelman, David
name: Podgornik, Rudolf
Publisher: name: arXiv
Year: 2023
Subjects: subject: Soft Condensed Matter (cond-mat.soft)
subject: Biological Physics (physics.bio-ph)
subject: Chemical Physics (physics.chem-ph)
subject: FOS: Physical sciences

description: We study the effects of charge-regulated acid/base equilibrium on the swelling of polyelectrolyte gels, by considering a combination of the Poisson-Boltzmann theory and a two-site charge-regulation model based on the Langmuir adsorption isotherm. By exploring the volume change as a function of salt concentration for both nano-gels and micro-gels, we identify conditions where the gel volume exhibits a discontinuous swelling transition. This transition is driven exclusively by the charge-regulation mechanism and is characterized by a closed-loop phase diagram. Our predictions can be tested experimentally for polypeptide gels.
High nucleosome occupancy is encoded at X-linked gene promoters in C. elegans
Creators: name: Lieb, J. D.
name: Ercan, S.
name: Lubling, Y.
name: Segal, E.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2011

description: We mapped nucleosome occupancy by paired-end Illumina sequencing in C. elegans embryonic cells, adult somatic cells, and a mix of adult somatic and germ cells. In all three samples, the nucleosome occupancy of gene promoters on the X chromosome differed from autosomal promoters. While both X and autosomal promoters exhibit a typical nucleosome-depleted region upstream of transcript start sites and a well-positioned +1 nucleosome, X-linked gene promoters on average exhibit higher nucleosome occupancy relative to autosomal promoters. We show that the difference between X and autosomes does not depend on the somatic dosage compensation machinery. Instead, the chromatin difference at promoters is partly encoded by DNA sequence, because a model trained on nucleosome sequence preferences from S. cerevisiae in vitro data recapitulate nearly completely the experimentally observed difference between X and autosomal promoters. The model predictions also correlate very well with experimentally determined occupancy values genome-wide. The nucleosome occupancy differences observed on X promoters may bear on mechanisms of X chromosome dosage compensation in the soma, and chromosome-wide repression of X in the germline.
Scalar products in GL(3)-based models with trigonometric R-matrix. Determinant representation
Creators: name: Slavnov, N. A.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Mathematical Physics (math-ph)
subject: FOS: Physical sciences

description: We study quantum integrable GL(3)-based models with a trigonometric R-matrix solvable by the nested algebraic Bethe ansatz. We derive a determinant representation for a special case of scalar products of Bethe vectors. This representation allows one to find a determinant formula for the form factor of one of the monodromy matrix entries. We also point out essential difference between form factors in the models with the trigonometric R-matrix and their analogs in GL(3)-invariant models.
description: 27 pages; typos corrected
Two surface plasmon decay of plasma oscillations
Creators: name: Kluge, Thomas
name: Metzkes, Josefine
name: Zeil, Karl
name: Bussmann, Michael
name: Schramm, Ulrich
name: Cowan, Thomas E.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Plasma Physics (physics.plasm-ph)
subject: FOS: Physical sciences

description: The interaction of ultra-intense lasers with solid foils can be used to accelerate ions to high energies well exceeding 60 MeV. The non-linear relativistic motion of electrons in the intense laser radiation leads to their acceleration and later to the acceleration of ions. Ions can be accelerated from the front surface, the foil interior region, and the foil rear surface (TNSA, most widely used), or the foil may be accelerated as a whole if sufficiently thin (RPA). Here, we focus on the most widely used mechanism for laser ion-acceleration of TNSA. Starting from perfectly flat foils we show by simulations how electron filamentation at or inside the solid leads to a spatial modulations in the ions. The exact dynamics depend very sensitively on the chosen initial parameters which has a tremendous effect on electron dynamics. In the case of step-like density gradients we find evidence that suggests a two-surface-plasmon decay of plasma oscillations triggering a Raileigh-Taylor-like instability.
Low-coverage sequencing: Implications for design of complex trait association studies
Creators: name: Boehnke, M.
name: Kang, H. M.
name: Li, Y.
name: Abecasis, G. R.
name: Sidore, C.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2011

description: New sequencing technologies allow genomic variation to be surveyed in much greater detail than previously possible. While detailed analysis of a single individual typically requires deep sequencing, when many individuals are sequenced it is possible to combine shallow sequence data across individuals to generate accurate calls in shared stretches of chromosome. Here, we show that, as progressively larger numbers of individuals are sequenced, increasingly accurate genotype calls can be generated for a given sequence depth. We evaluate the implications of low-coverage sequencing for complex trait association studies. We systematically compare study designs based on genotyping of tagSNPs, sequencing of many individuals at depths ranging between 2× and 30×, and imputation of variants discovered by sequencing a subset of individuals into the remainder of the sample. We show that sequencing many individuals at low depth is an attractive strategy for studies of complex trait genetics. For example, for disease-associated variants with frequency >0.2%, sequencing 3000 individuals at 4× depth provides similar power to deep sequencing of >2000 individuals at 30× depth but requires only ∼20% of the sequencing effort. We also show low-coverage sequencing can be used to build a reference panel that can drive imputation into additional samples to increase power further. We provide guidance for investigators wishing to combine results from sequenced, genotyped, and imputed samples.
MOESM1 of Development of caesarean section prediction models: secondary analysis of a prospective cohort study in two sub-Saharan African countries
Creators: name: Hayala Souza
name: Gleici Perdoná
name: Marcolin, Alessandra
name: Lawal Oyeneyin
name: Olufemi Oladapo
name: Kidza Mugerwa
name: Souza, João
Publisher: name: figshare
Year: 2019
Subjects: subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Inorganic Chemistry
subject: FOS: Chemical sciences
subject: Science Policy

description: Additional file 1: Table S1. Description of the fixed variables considered in the bivariate analysis step Table S2. Description of the dynamic variables considered in the bivariate analysis Table S3. Description of variables recorded throughout the labour considered in the univariate analysis Table S4. P-value for Hosmer-Lemeshow test in each of the estimated models Figure S1. Analysis flow diagram Figure S2. ROC curves for models in the training sample (left column) and test sample (right column).
Una història d'èxit en ciència ciutadana - BioMARató 2021: resultats destacats
Creators: name: Salvador, Xavier
name: Piera, Jaume
name: Liñán, Sonia
name: Justamante, Ángela
Publisher: name: Zenodo
Year: 2023
Subjects: ciència ciutadana
BioMARató
biodiversitat marina
observatoris ciutadans
ciència
BioBlitz
dades obertes

description: Aquesta infografia resumeix els resultats de la primera edició de la BioMARató-Platges amb vida, un dels majors esdeveniments de ciència ciutadana i observacions marines a Catalunya. Es va tractar d'una activitat impulsada per l'Institut de Ciències del Mar (ICM) juntament amb el projecte Cos4Cloud, l'empresa Anèl·lides, serveis ambientals marins, l’associació mediambiental Xatrac i dos centres de submarinisme: Oceánicos, i Plàncton Diving i l'ajuntament de Calonge i Sant Antoni, que busca promoure la conservació i la sensibilització al voltant de l'ecosistema marí.
Spin alignment of vector mesons by glasma fields
Creators: name: Kumar, Avdhesh
name: Müller, Berndt
name: Yang, Di-Lun
Publisher: name: arXiv
Year: 2023
Subjects: subject: Nuclear Theory (nucl-th)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: We explain how spin alignment of vector mesons can be induced by background fields, such as electromagnetic fields or soft gluon fields. Our study is based on the quantum kinetic theory of spinning quarks and antiquarks and incorporates the relaxation of the dynamically generated spin polarization. The spin density matrix of vector mesons is obtained by quark coalescence via the Wigner function and kinetic equation. Our approach predicts a local spin correlation that is distinct from the non-local expressions previously obtained in phenomenological derivations. We estimate the magnitude of such local correlations in the glasma model of the preequilibrium phase of relativistic heavy ion collisions. It is found that the resulting spin alignment could be greatly enhanced and may be comparable to the experimental measurement in order of magnitude. We further propose new phenomenological scenarios to qualitatively explain the transverse-momentum and centrality dependence of spin alignment in a self-consistent framework.
description: 47 pages, 9 figures, minor revisions and extension, journal version
Supplementary file. Original museum material of fossil Coleoptera (Tenebrionidae and identified as Tenebrionidae) from Fossil Lagerstätte Willershausen, deposited in the Geoscience Museum at the Georg-August University in Göttingen
Creators: name: Nabozhenko, Maxim V.
name: Shaw, Josh Jenkins
name: Gehler, Alexander
name: Kaulfuss, Uwe
Publisher: name: Zenodo
Year: 2023
Subjects: Tenebrionodae, Elateridae, Cerambycidae, fossil beetles, Late Pliocene, Willershausen Lagerstätte, Germany

description: The table contents the orinal museum material on Coleoptera (compressed prints) from the Fossil Lagerstätte Willershausen (51.783724 N, 10.113421 E, ca. 30 km north of Göttingen, Lower Saxony, Germany; Late Pliocene, Piacenzian, 3.6 – 2.588 Mya). Taxonomic position and labels data are presented for each specimen, belonging to the family Tenebrionidae or determined as Tenebrionidae by Erasmus Gersdorf (1967, 1971, 1976).
description: supplementary material for the paper: Euboeus mimonti Boieldieu, 1865, the oldest record of an extant species of Tenebrionidae (Coleoptera) and notes on other species identified as darkling beetles from the Late Pliocene of Willershausen (Germany)
Gravitational Waves from Preheating in Gauss-Bonnet Inflation
Creators: name: Bourakadi, K. El
name: Ferricha-Alami, M.
name: Filali, H.
name: Sakhi, Z.
name: Bennai, M.
Publisher: name: arXiv
Year: 2022
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: We study gravitational wave production in an expanding Universe during the first stages following inflation, and investigate the consequences of the Gauss-Bonnet term on the inflationary parameters for a power-law inflation model with a GB coupling term. Moreover, we perform the analyses on the preheating parameters involving the number of e-folds $N_{pre}$, and the temperature of thermalization $T_{th},$ and show that it's sensitive to the parameters $n$, and $γ$, the parameter $γ$ is proposed to connect the density energy at the end of inflation to the preheating energy density. We set a correlation of gravitational wave energy density spectrum with the spectral index $n_{s}$ detected by the cosmic microwave background experiments$.$ The density spectrum $Ω_{gw}$ shows good consistency with observation for $γ= 10^{3}$ and $10^{6}$. Our findings suggest that the generation of gravitational waves (GWs) during preheating can satisfy the constraints from Planck's data.
Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity
Creators: name: Winter, D.
name: Wang, T.
name: Sheffield, N. C.
name: Showers, K. A.
name: Clarke, N. D.
name: Grasfeder, L. L.
name: Zhang, Z.
name: McDaniell, R. M.
name: Iyer, V. R.
name: Lieb, J. D.
name: Keefe, D.
name: Graf, S.
name: Furey, T. S.
name: Song, L.
name: Birney, E.
name: Liu, Z.
name: Vales, T.
name: Huss, M.
name: Lee, B.-K.
name: London, D.
name: Shibata, Y.
name: Crawford, G. E.
name: Boyle, A. P.
name: Simon, J. M.
name: Giresi, P. G.
name: Zhang, Z.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2011

description: The human body contains thousands of unique cell types, each with specialized functions. Cell identity is governed in large part by gene transcription programs, which are determined by regulatory elements encoded in DNA. To identify regulatory elements active in seven cell lines representative of diverse human cell types, we used DNase-seq and FAIRE-seq (Formaldehyde Assisted Isolation of Regulatory Elements) to map “open chromatin.” Over 870,000 DNaseI or FAIRE sites, which correspond tightly to nucleosome-depleted regions, were identified across the seven cell lines, covering nearly 9% of the genome. The combination of DNaseI and FAIRE is more effective than either assay alone in identifying likely regulatory elements, as judged by coincidence with transcription factor binding locations determined in the same cells. Open chromatin common to all seven cell types tended to be at or near transcription start sites and to be coincident with CTCF binding sites, while open chromatin sites found in only one cell type were typically located away from transcription start sites and contained DNA motifs recognized by regulators of cell-type identity. We show that open chromatin regions bound by CTCF are potent insulators. We identified clusters of open regulatory elements (COREs) that were physically near each other and whose appearance was coordinated among one or more cell types. Gene expression and RNA Pol II binding data support the hypothesis that COREs control gene activity required for the maintenance of cell-type identity. This publicly available atlas of regulatory elements may prove valuable in identifying noncoding DNA sequence variants that are causally linked to human disease.
Isotope systematics and crustal evolution of the Archean Winnipeg River terrane, Superior Province, Canada
Creators: name: STRONG, JACOB WALTER DOUGLAS
Publisher: name: Monash University
Year: 2022
Subjects: Isotope geochemistry
Geochronology

description: The Superior Province in Canada is Earth’s largest Archean craton (4.0-2.5 billion years), but its early geological history is poorly constrained. My thesis presents new radiogenic isotope data for inherited and detrital zircons from the central Winnipeg River terrane, which reveal a previously unrecognized 3.8-3.4 billion year record. The early history of the terrane overlaps with two other crustal blocks on the northern and southern edges of the province. The evidence suggests that between 3.8-2.7 billion years ago initial continental growth was followed by the breakup of crustal blocks and their subsequent reassembly.
Open Access časopisy: Přehled pro Lékařskou fakultu v Plzni UK
Creators: name: Stupavská, Libuše
Publisher: name: Zenodo
Year: 2020
Subjects: open access
gold open access
impact factor

description: Přehled open access a hybridních časopisů, ve kterých nejčastěji publikovali autoři z Lékařské fakulty v Plzni Univerzity Karlovy. Údaje pocházejí z OBD z období od ledna 2019 do září 2020. Časopisy jsou řazeny podle hodnoty impact factoru. Přehled byl součástí Týdne otevřeného přístupu 2020.
Chiral Lagrangians for spin-$\frac{1}{2}$ and spin-$\frac{3}{2}$ doubly charmed baryons
Creators: name: Liu, Hao
name: Zou, Yuan-He
name: Liu, Yan-Rui
name: Jiang, Shao-Zhou
Publisher: name: arXiv
Year: 2023
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: The relativistic chiral Lagrangians for both spin-$\frac{1}{2}$ and spin-$\frac{3}{2}$ doubly charmed baryons are constructed up to the order $\mathcal{O}(p^{4})$. From $\mathcal{O}(p^{2})$ to $\mathcal{O}(p^{4})$, there are 19, 74, and 452 independent terms in the two-flavor case and 25, 112, and 864 independent terms in the three-flavor case. The chiral Lagrangians in the heavy diquark limit are also obtained. From $\mathcal{O}(p^{2})$ to $\mathcal{O}(p^{4})$, there are 7, 23, and 118 independent terms in the two-flavor case and 8, 31, and 189 independent terms in the three-flavor case. We present the low-energy constant relations between the relativistic case and the case in the heavy diquark limit up to the order $\mathcal{O}(p^{3})$. With the heavy diquark-antiquark symmetry, the low-energy constant relations between the doubly charmed baryon case and the heavy-light meson case are also obtained up to the order $\mathcal{O}(p^{3})$.
description: 28 pages
Una historia de éxito en ciencia ciudadana, BioMARató 2022: resultados destacados
Creators: name: Salvador, Xavier
name: Piera, Jaume
name: Liñán, Sonia
name: Justamante, Ángela
Publisher: name: Zenodo
Year: 2023
Subjects: ciencia ciudadana
BioMARató
observatorio ciudadano
ciencia
datos abiertos
biodiversidad marina

description: Esta infografía resume los resultados de la segunda edición de la BioMARató-Playas con vida, uno de los mayores acontecimientos de ciencia ciudadana y observaciones marinas en Cataluña. La BioMARató es una actividad impulsada por el ICM-CSIC. Las entidades encargadas de dinamizar las actividades son Anèl·lides – Serveis ambientals marins, la Federación Catalana de Actividades Subacuáticas (FECDAS), Xatrac y Plàncton Diving. Además, colaboran los proyectos europeos Horizon2020 Cos4Cloud y MINKE, coordinados por el ICM-CSIC, los centros de buceo iDive, Saita Diving, Vanas Dive, Underwater Barcelona y OCEANICOS.
Rare $B$ decays using lattice QCD form factors
Creators: name: Horgan, R. R.
name: Liu, Z.
name: Meinel, S.
name: Wingate, M.
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Physics - Lattice (hep-lat)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: In this write-up we review and update our recent lattice QCD calculation of $B \to K^*$, $B_s \to ϕ$, and $B_s \to K^*$ form factors [arXiv:1310.3722]. These unquenched calculations, performed in the low-recoil kinematic regime, provide a significant improvement over the use of extrapolated light cone sum rule results. The fits presented here include further kinematic constraints and estimates of additional correlations between the different form factor shape parameters. We use these form factors along with Standard Model determinations of Wilson coefficients to give Standard Model predictions for several observables [arXiv:1310.3887]. The modest improvements to the form factor fits lead to improved determinations of $F_L$, the fraction of longitudinally polarized vector mesons, but have little effect on most other observables.
description: Contribution to the Proceedings of the 32nd International Symposium on Lattice Field Theory (LATTICE 2014), 23-28 June 2014, Columbia University. 13 pages (7 pp to appear in Proceedings of Science + 6 pp of supplementary details). Fits in v2 use block-diagonal correlations (results not significantly changed). v2 corrects a permutation of columns in Table 8/11 of v1/v2. Reference added
Transient translation symmetry breaking via quartic-order negative light-phonon coupling at the Brillouin zone boundary in KTaO${}_{3}$
Creators: name: Pueyo, Adrián Gómez
name: Subedi, Alaska
Publisher: name: arXiv
Year: 2023
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: KTaO${}_{3}$ presents a rich hyper-Raman spectrum originating from two-phonon processes at the Brillouin zone boundary, indicating the possibility of driving these phonon modes using intense midinfrared laser sources. We obtained the coupling of light to the highest-frequency longitudinal optic phonon mode $Q_{\rm{HY}}$ at the $X$ $(0,0, \frac{1}{2})$ point by first principles calculations of the total energy as a function of the phonon coordinate $Q_{\rm{HY}}$ and electric field $E$. We find that the energy curve as a function of $Q_{\rm{HY}}$ softens for finite values of electric field, indicating the presence of $Q_{\rm{HY}}^2 E^2$ nonlinearity with negative coupling coefficient. We studied the feasibility of utilizing this nonlinearity to transiently break the translation symmetry of the material by making the $Q_{\rm{HY}}$ mode unstable with an intense midinfrared pump pulse. We also considered the possibility that nonlinear phonon-phonon couplings can excite the lowest-frequency phonon coordinates $Q_{\rm{LZ}}$ and $Q_{\rm{LX}}$ at $X$ when the $Q_{\rm{HY}}$ mode is externally driven. The nonlinear phonon-phonon couplings were also obtained from first principles via total-energy calculations as a function of the phonon coordinates, and these were used to construct the coupled classical equations of motion for the phonon coordinates in the presence of an external pump term on $Q_{\rm{HY}}$. We numerically solved them for a range of pump frequencies and amplitudes and found three regimes where the translation symmetry is broken: i) rectification of the lowest-frequency coordinates due to large amplitude oscillation of the $Q_{\rm{HY}}$ coordinate about its equilibrium position, ii) rectification of only the $Q_{\rm{HY}}$ coordinate without displaced oscillations of the lowest-frequency coordinates, and iii) rectification of all three coordinates.
description: Updated the paper and the DOI
On the Neural Representation for Adversarial Attack and Defense
Creators: name: Xu, Qiuling
Publisher: name: Purdue University Graduate School
Year: 2023
Subjects: classificationCode: 461101
subject: Adversarial machine learning

description: Neural representations are high-dimensional embeddings generated during the feed-forward process of neural networks. These embeddings compress raw input information and extract abstract features beneficial for downstream tasks. However, effectively utilizing these representations poses challenges due to their inherent complexity. This complexity arises from the non-linear relationship between inputs and neural representations, as well as the diversity of the learning process.In this thesis, we propose effective methods to utilize neural representations for adversarial attack and defense. Our approach generally involves decomposing complex neural representations into smaller, more analyzable parts. We also seek general patterns emerging during learning to better understand the semantic meaning associated with neural representations.We demonstrate that formalizing neural representations can reveal models' weaknesses and aid in defending against poison attacks. Specifically, we define a new type of adversarial attack using neural style, a special component of neural representation. This new attack uncovers novel aspects of the models' vulnerabilities. Furthermore, we develop an interpretation of neural representations by approximating their marginal distribution, treating intermediate neurons as feature indicators. By properly harnessing these rich feature indicators, we address scalability and imperceptibility issues related to pixel-wise bounds.Finally, we discover that neural representations contain crucial information about how neural networks make decisions. Leveraging the general patterns in neural representations, we design algorithms to remove unwanted and harmful functionalities from neural networks, thereby mitigating poison attacks.
Una història d'èxit en ciència ciutadana - BioMARató 2022: resultats destacats
Creators: name: Salvador, Xavier
name: Piera, Jaume
name: Liñán, Sonia
name: Justamante, Ángela
Publisher: name: Zenodo
Year: 2023
Subjects: ciència ciutadana
BioMARató
biodiversitat marina
observatoris ciutadans
ciència
dades obertes

description: Aquesta infografia resumeix els resultats de la segona edició de la BioMARató-Platges amb vida, un dels majors esdeveniments de ciència ciutadana i observacions marines a Catalunya. La BioMARató és una activitat impulsada per l’ICM-CSIC. Les entitats encarregades de dinamitzar les activitats són Anèl·lides – Serveis ambientals marinsla Federació Catalana d'Activitats Subaquàtiques (FECDAS), Xatrac i Plàncton Diving. A més, col·laboren els projectes europeus Horizon2020 Cos4Cloud i MINKE, coordinats per l’ICM-CSIC, els centres de busseig iDive, Saita Diving, Vanas Dive, Underwater Barcelona i OCEANICOS.
Characterization of symmetry-protected topological phases in polymerized models by trajectories of Majorana stars
Creators: name: Yang, Chao
name: Guo, Huaiming
name: Fu, Li-Bin
name: Chen, Shu
Publisher: name: arXiv
Year: 2015
Subjects: subject: Other Condensed Matter (cond-mat.other)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: By using Majorana's stellar representation, we give a clear geometrical interpretation of the topological phases of inversion-symmetric polymerized models by mapping the Bloch states of multi-band systems to Majorana stars on the Bloch sphere. While trajectories of Majorana stars of a filled Bloch band exhibit quite different geometrical structures for topologically trivial and nontrivial phases, we further demonstrate that these structures are uniquely determined by distributions of Majorana stars of two high-symmetrical momentum states, which have different parities for topologically different states.
description: 6 pages, 6 figures
Curcumin modulates multiple cell death, matrix metalloproteinase activation and cardiac protein release in susceptible and resistant plasmodium berghei-infected mice.
Creators: name: Olanlokun, John O.
name: Abiodun, Wisdom Oshireku
name: Ebenezer, Oluwakemi
name: Koorbanally, Neil A.
name: Olorunsogo, Olufunso Olabode
Publisher: name: Mangosuthu University of Technology (MUT)
Year: 2023
Subjects: Medical biotechnology not elsewhere classified
Medical biotechnology diagnostics (incl. biosensors)

description: Pro-inflammatory signaling, cell death, and metalloproteinases activation are events in Plasmodium infection. However, it is not known if treatment with mefloquine (MF), and curcumin (CM) supplementation, will modulate these conditions. Malaria was induced in two different studies using susceptible (NK 65, study 1) and resistant (ANKA, study 2) strains of mouse malaria parasites (Plasmodium berghei) in thirty male Swiss mice (n = 5) in each study. Following confirmation of parasitemia, mice received 10 mL/kg distilled water (infected control), MF (10 mg/kg), MF and CM (25 mg/kg), MF and CM (50 mg/kg), CM (25 mg/kg) and CM (50 mg/kg). Five mice (not infected) were used as control. After treatment, the animals were sacrificed, serum obtained and liver mito?chondria were isolated. Serum Tumour Necrosis Factor alpha (TNF-α), C-reactive protein (CRP), Interleukins-1 beta (IL-1β) and Interleukins-6 (IL-6) as well as caspases-3, 9 (C3 and C9), p53, serum troponin I (TI) and cre?atine kinase (CK), were assayed using ELISA techniques. Mitochondrial membrane permeability transition (mPT) pore opening, mitochondrial F0F1 ATPase activity, and lipid peroxidation (mLPO) were determined spectro?photometrically. Matrix metalloproteinases 2 (MMP-2) and 9 (MMP-9) expressions were determined using electrophoresis. CM supplementation (25 mg/kg) significantly decreased serum p53, TNF-α, CRP and IL-6 compared with MF. In the resistant model, CM prevented mPT pore opening, significantly decreased F0F1 ATPase activity and mLPO. MF activated caspase-3 while supplementation with CM significantly decreased this effect. Furthermore, MMP-2 and MMP-9 were selectively expressed in the susceptible model. Malarial treatment with mefloquine elicits different cell death responses while supplementation with curcumin decreased TI level and CK activities.
Interaction-Free Measurements: A Complex Nonlinear Explanation
Creators: name: Cardoso, António
name: Cordovil, João L.
name: Croca, José R.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Quantum Physics (quant-ph)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: In this paper we show that interaction-free measurements, which have been object of much discussion in the last few decades, can be explained in a natural and intuitive way in the framework of complex nonlinear quantum physics, contrary to what is claimed by some orthodox authors that present them as incomprehensible, mind-boggling experiments.
description: 9 pages, 5 figures
Simple cubic random-site percolation thresholds for neighborhoods containing fourth-nearest neighbors
Creators: name: Malarz, K.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: Mathematical Physics (math-ph)
subject: FOS: Physical sciences

description: In the paper random-site percolation thresholds for simple cubic lattice with sites' neighborhoods containing next-next-next-nearest neighbors (4NN) are evaluated with Monte Carlo simulations. A recently proposed algorithm with low sampling for percolation thresholds estimation [Bastas et al., arXiv:1411.5834] is implemented for the studies of the top-bottom wrapping probability. The obtained percolation thresholds are $p_C(\text{4NN})=0.31160(12)$, $p_C(\text{4NN+NN})=0.15040(12)$, $p_C(\text{4NN+2NN})=0.15950(12)$, $p_C(\text{4NN+3NN})=0.20490(12)$, $p_C(\text{4NN+2NN+NN})=0.11440(12)$, $p_C(\text{4NN+3NN+NN})=0.11920(12)$, $p_C(\text{4NN+3NN+2NN})=0.11330(12)$, $p_C(\text{4NN+3NN+2NN+NN})=0.10000(12)$, where 3NN, 2NN, NN stands for next-next-nearest neighbors, next-nearest neighbors, and nearest neighbors, respectively. As an SC lattice with 4NN neighbors may be mapped onto two independent interpenetrated SC lattices but with two times larger lattice constant the percolation threshold $p_C$(4NN) is exactly equal to $p_C$(NN). The simplified Bastas et al. method allows for reaching uncertainty of the percolation threshold value $p_C$ similar to those obtained with classical method but ten times faster.
description: 5 pages, 3 figures
Identification of weakly coupled multiphysics problems. Application to the inverse problem of electrocardiography
Creators: name: Corrado, Cesare
name: Gerbeau, Jean-Frédéric
name: Moireau, Philippe
Publisher: name: arXiv
Year: 2015
Subjects: subject: Numerical Analysis (math.NA)
subject: FOS: Mathematics

description: This work addresses the inverse problem of electrocardiography from a new perspective, by combining electrical and mechanical measurements. Our strategy relies on the defini-tion of a model of the electromechanical contraction which is registered on ECG data but also on measured mechanical displacements of the heart tissue typically extracted from medical images. In this respect, we establish in this work the convergence of a sequential estimator which combines for such coupled problems various state of the art sequential data assimilation methods in a unified consistent and efficient framework. Indeed we ag-gregate a Luenberger observer for the mechanical state and a Reduced Order Unscented Kalman Filter applied on the parameters to be identified and a POD projection of the electrical state. Then using synthetic data we show the benefits of our approach for the estimation of the electrical state of the ventricles along the heart beat compared with more classical strategies which only consider an electrophysiological model with ECG measurements. Our numerical results actually show that the mechanical measurements improve the identifiability of the electrical problem allowing to reconstruct the electrical state of the coupled system more precisely. Therefore, this work is intended to be a first proof of concept, with theoretical justifications and numerical investigations, of the ad-vantage of using available multi-modal observations for the estimation and identification of an electromechanical model of the heart.
The Impact of Frame-Dropping on Performance and Energy Consumption for Multi-Object Tracking
Creators: name: Henning, Matti
name: Buchholz, Michael
name: Dietmayer, Klaus
Publisher: name: arXiv
Year: 2023
Subjects: subject: Robotics (cs.RO)
subject: FOS: Computer and information sciences

description: The safety of automated vehicles (AVs) relies on the representation of their environment. Consequently, state-of-the-art AVs employ potent sensor systems to achieve the best possible environment representation at all times. Although these high-performing systems achieve impressive results, they induce significant requirements for the processing capabilities of an AV's computational hardware components and their energy consumption. To enable a dynamic adaptation of such perception systems based on the situational perception requirements, we introduce a model-agnostic method for the scalable employment of single-frame object detection models using frame-dropping in tracking-by-detection systems. We evaluate our approach on the KITTI 3D Tracking Benchmark, showing that significant energy savings can be achieved at acceptable performance degradation, reaching up to 28% reduction of energy consumption at a performance decline of 6.6% in HOTA score.
description: V1: Accepted for publication at the IEEE Intelligent Vehicle Symposium, 2023 V2: Added DOI 10.1109/IV55152.2023.10186653
The Mosquito incident and the need-(not-)to-know
Creators: name: Svozil, Karl
Publisher: name: arXiv
Year: 2022
Subjects: subject: History and Philosophy of Physics (physics.hist-ph)
subject: FOS: Physical sciences

description: I am reporting here how professor Cristian Sorin Calude, henceforth called Cris, became involved in the "Mosquito incident". More generally, the relationship between the single individual vis-a-vis the state or collective is reviewed, with special emphasis to need-(not)-to-know secrets.
Three-body recombination of two-component cold atomic gases into deep dimers in an optical model
Creators: name: Mikkelsen, M.
name: Jensen, A. S.
name: Fedorov, D. V.
name: Zinner, N. T.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Quantum Gases (cond-mat.quant-gas)
subject: Nuclear Theory (nucl-th)
subject: Atomic Physics (physics.atom-ph)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We consider three-body recombination into deep dimers in a mass-imbalanced two-component atomic gas. We use an optical model where a phenomenological imaginary potential is added to the lowest adiabatic hyper-spherical potential. The consequent imaginary part of the energy eigenvalue corresponds to the decay rate or recombination probability of the three-body system. The method is formulated in details and the relevant qualitative features are discussed as functions of scattering lengths and masses. We use zero-range model in analyses of recent recombination data. The dominating scattering length is usually related to the non-equal two-body systems. We account for temperature smearing which tends to wipe out the higher-lying Efimov peaks. The range and the strength of the imaginary potential determine positions and shapes of the Efimov peaks as well as the absolute value of the recombination rate. The Efimov scaling between recombination peaks is calculated and shown to depend on both scattering lengths. Recombination is predicted to be largest for heavy-heavy-light systems. Universal properties of the optical parameters are indicated. We compare to available experiments and find in general very satisfactory agreement.
description: 16 pages, 12 figures, 3 tables, revised version
Bifundamental Superfluids from Holography
Creators: name: Arean, Daniel
name: Tarrio, Javier
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: We study the holographic dual of a (2+1)-dimensional s-wave superfluid that breaks an abelian U(1) x U(1) global symmetry group to the diagonal U(1)_V. The model is inspired by Sen's tachyonic action, and the operator that condenses transforms in the bifundamental representation of the symmetry group. We focus on two configurations: the first one describes a marginal operator, and the phase diagram at finite temperature contains a first or a second order phase transition, depending on the parameters that determine the theory. In the second model the operator is relevant and the finite temperature transitions are always second order. In the latter case the conductivity for the current associated to the broken symmetry shows quasiparticle excitations at low temperatures, with mass given by the width of the superconducting gap. The suppression of spectral weight at low frequencies is also observed in the conductivity associated to the conserved symmetry, for which the DC value decreases as the temperature is reduced.
description: 30 pages, 14 figures; v2: refs. added, plots and discussion improved, typos corrected, published version
DeePMD-kit v2: A software package for Deep Potential models
Creators: name: Zeng, Jinzhe
name: Zhang, Duo
name: Lu, Denghui
name: Mo, Pinghui
name: Li, Zeyu
name: Chen, Yixiao
name: Rynik, Marián
name: Huang, Li'ang
name: Li, Ziyao
name: Shi, Shaochen
name: Wang, Yingze
name: Ye, Haotian
name: Tuo, Ping
name: Yang, Jiabin
name: Ding, Ye
name: Li, Yifan
name: Tisi, Davide
name: Zeng, Qiyu
name: Bao, Han
name: Xia, Yu
name: Huang, Jiameng
name: Muraoka, Koki
name: Wang, Yibo
name: Chang, Junhan
name: Yuan, Fengbo
name: Bore, Sigbjørn Løland
name: Cai, Chun
name: Lin, Yinnian
name: Wang, Bo
name: Xu, Jiayan
name: Zhu, Jia-Xin
name: Luo, Chenxing
name: Zhang, Yuzhi
name: Goodall, Rhys E. A.
name: Liang, Wenshuo
name: Singh, Anurag Kumar
name: Yao, Sikai
name: Zhang, Jingchao
name: Wentzcovitch, Renata
name: Han, Jiequn
name: Liu, Jie
name: Jia, Weile
name: York, Darrin M.
name: E, Weinan
name: Car, Roberto
name: Zhang, Linfeng
name: Wang, Han
Publisher: name: arXiv
Year: 2023
Subjects: subject: Chemical Physics (physics.chem-ph)
subject: Atomic and Molecular Clusters (physics.atm-clus)
subject: FOS: Physical sciences
subject: J.2

description: DeePMD-kit is a powerful open-source software package that facilitates molecular dynamics simulations using machine learning potentials (MLP) known as Deep Potential (DP) models. This package, which was released in 2017, has been widely used in the fields of physics, chemistry, biology, and material science for studying atomistic systems. The current version of DeePMD-kit offers numerous advanced features such as DeepPot-SE, attention-based and hybrid descriptors, the ability to fit tensile properties, type embedding, model deviation, Deep Potential - Range Correction (DPRc), Deep Potential Long Range (DPLR), GPU support for customized operators, model compression, non-von Neumann molecular dynamics (NVNMD), and improved usability, including documentation, compiled binary packages, graphical user interfaces (GUI), and application programming interfaces (API). This article presents an overview of the current major version of the DeePMD-kit package, highlighting its features and technical details. Additionally, the article benchmarks the accuracy and efficiency of different models and discusses ongoing developments.
description: 51 pages, 2 figures
A citizen science success story - BioMARató 2022: noteworthy results
Creators: name: Salvador, Xavier
name: Piera, Jaume
name: Liñán, Sonia
name: Justamante, Ángela
Publisher: name: Zenodo
Year: 2023
Subjects: citizen science
marine biodiversity
citizen observatory
science
open data
BioMARató

description: This infographic summarises the results of the second edition of the BioMARató-Beaches with life, one of the most significant citizen science and marine observations events in Catalonia. BioMARató is an activity promoted by the ICM-CSIC. The entities responsible for organising the activities are Anèl-lides - Serveis ambientals marins, the Catalan Federation of Underwater Activities (FECDAS), Xatrac and Plàncton Diving. In addition, the European Horizon2020 projects Cos4Cloud and MINKE, coordinated by the ICM-CSIC, the diving centres iDive, Saita Diving, Vanas Dive, Underwater Barcelona and OCEANICOS.
Intensity effects of light coupling to one- or two-atom arrays of infinite extent
Creators: name: Robicheaux, F.
name: Suresh, Deepak A.
Publisher: name: arXiv
Year: 2023
Subjects: subject: Quantum Physics (quant-ph)
subject: Atomic Physics (physics.atom-ph)
subject: FOS: Physical sciences

description: We theoretically and computationally investigate the behavior of infinite atom arrays when illuminated by nearly resonant light. We use higher order mean field equations to investigate the coherent reflection and transmission and incoherent scattering of photons from a single array and from a pair of arrays as a function of detuning for different values of the Rabi frequency. For the single array case, we show how increasing the light intensity changes the probabilities for these different processes. For example, the incoherent scattering probability initially increases with light intensity before decreasing at higher values. For a pair of parallel arrays at near resonant separation, the effects from increasing light intensity can become apparent with incredibly low intensity light. In addition, we derive the higher order mean field equations for these infinite arrays giving a representation that can be evaluated with a finite number of equations.
Characterizing non-Markovianity via quantum interferometric power
Creators: name: Dhar, Himadri Shekhar
name: Bera, Manabendra Nath
name: Adesso, Gerardo
Publisher: name: arXiv
Year: 2015
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: Non-Markovian evolution in open quantum systems is often characterized in terms of the backflow of information from environment to system and is thus an important facet in investigating the performance and robustness of quantum information protocols. In this work, we explore non-Markovianity through the breakdown of monotonicity of a metrological figure of merit, called the quantum interferometric power, which is based on the minimal quantum Fisher information obtained by local unitary evolution of one part of the system, and can be interpreted as a quantifier of quantum correlations beyond entanglement. We investigate our proposed non-Markovianity indicator in two relevant examples. First, we consider the action of a single-party dephasing channel on a maximally entangled two-qubit state, by applying the Jamiołkowski-Choi isomorphism. We observe that the proposed measure is consistent with established non-Markovianity quantifiers defined using other approaches based on dynamical divisibility, distinguishability, and breakdown of monotonicity for the quantum mutual information. Further, we consider the dynamics of two-qubit Werner states, under the action of a local, single-party amplitude damping channel, and observe that the nonmonotonic evolution of the quantum interferometric power is more robust than the corresponding one for entanglement in capturing the backflow of quantum information associated with the non-Markovian process. Implications for the role of non-Markovianity in quantum metrology and possible extensions to continuous variable systems are discussed.
description: 4 figures, 9 pages, REVTeX 4-1, close to published version