cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Oligotyping reveals differences between gut microbiomes of free-ranging sympatric namibian carnivores (Acinonyx jubatus, Canis mesomelas) on a bacterial species-like level
Creators: name: Menke, Sebastian
name: Wasimuddin
name: Meier, Matthias
name: Melzheimer, Jörg
name: Mfune, John K. E.
name: Heinrich, Sonja Kirsten
name: Thalwitzer, Susanne
name: Wachter, Bettina
name: Sommer, Simone
Publisher: name: Universität Ulm
Year: 2014
Subjects: subject: gut microbiome
subject: oligotyping
subject: cheetah (Acinonyx jubatus)
subject: black-backed jackal (Canis mesomelas)
subject: DDC 570 / Life sciences
subject: Bacteria
subject: Carnivores
subject: Cheetah
subject: Black-backed jackal
subject: Namibia
subject: Bakterien
subject: Karnivoren
subject: Gepard

description: Recent gut microbiome studies in model organisms emphasize the effects of intrinsic and extrinsic factors on the variation of the bacterial composition and its impact on the overall health status of the host. Species occurring in the same habitat might share a similar microbiome, especially if they overlap in ecological and behavioral traits. So far, the natural variation in microbiomes of free-ranging wildlife species has not been thoroughly investigated. The few existing studies exploring microbiomes through 16S rRNA gene reads clustered sequencing reads into operational taxonomic units (OTUs) based on a similarity threshold (e.g., 97%). This approach, in combination with the low resolution of target databases, generally limits the level of taxonomic assignments to the genus level. However, distinguishing natural variation of microbiomes in healthy individuals from “abnormal” microbial compositions that affect host health requires knowledge of the “normal” microbial flora at a high taxonomic resolution. This gap can now be addressed using the recently published oligotyping approach, which can resolve closely related organisms into distinct oligotypes by utilizing subtle nucleotide variation. Here, we used Illumina MiSeq to sequence amplicons generated from the V4 region of the 16S rRNA gene to investigate the gut microbiome of two free-ranging sympatric Namibian carnivore species, the cheetah (Acinonyx jubatus) and the black-backed jackal (Canis mesomelas). Bacterial phyla with proportions >0.2% were identical for both species and included Firmicutes, Fusobacteria, Bacteroidetes, Proteobacteria and Actinobacteria. At a finer taxonomic resolution, black-backed jackals exhibited 69 bacterial taxa with proportions ≥0.1%, whereas cheetahs had only 42. Finally, oligotyping revealed that shared bacterial taxa consisted of distinct oligotype profiles. Thus, in contrast to 3% OTUs, oligotyping can detect fine-scale taxonomic differences between microbiomes.
Remarks on pseudo-vertex-transitive graphs with small diameter
Creators: name: Koolen, Jack H.
name: Lee, Jae-Ho
name: Tan, Ying-Ying
Publisher: name: arXiv
Year: 2021
Subjects: subject: Combinatorics (math.CO)
subject: FOS: Mathematics
subject: 05E30

description: Let $Γ$ denote a $Q$-polynomial distance-regular graph with vertex set $X$ and diameter $D$. Let $A$ denote the adjacency matrix of $Γ$. For a vertex $x\in X$ and for $0 \leq i \leq D$, let $E^*_i(x)$ denote the projection matrix to the $i$th subconstituent space of $Γ$ with respect to $x$. The Terwilliger algebra $T(x)$ of $Γ$ with respect to $x$ is the semisimple subalgebra of $\mathrm{Mat}_X(\mathbb{C})$ generated by $A, E^*_0(x), E^*_1(x), \ldots, E^*_D(x)$. Let $V$ denote a $\mathbb{C}$-vector space consisting of complex column vectors with rows indexed by $X$. We say $Γ$ is pseudo-vertex-transitive whenever for any vertices $x,y \in X$, there exists a $\mathbb{C}$-vector space isomorphism $ρ:V\to V$ such that $(ρA - A ρ)V=0$ and $(ρE^*_i(x) - E^*_i(y)ρ)V=0$ for all $0\leq i \leq D$. In this paper, we discuss pseudo-vertex transitivity for distance-regular graphs with diameter $D\in \{2,3,4\}$. For $D=2$, we show that a strongly regular graph is pseudo-vertex-transitive if and only if all its local graphs have the same spectrum. For $D = 3$, we consider the Taylor graphs and show that they are pseudo-vertex transitive. For $D=4$, we consider the antipodal tight graphs and show that they are pseudo-vertex transitive.
description: 30 pages
Dynamic Placement in Refugee Resettlement
Creators: name: Ahani, Narges
name: Gölz, Paul
name: Procaccia, Ariel D.
name: Teytelboym, Alexander
name: Trapp, Andrew C.
Publisher: name: arXiv
Year: 2021
Subjects: subject: Computer Science and Game Theory (cs.GT)
subject: Physics and Society (physics.soc-ph)
subject: FOS: Computer and information sciences
subject: FOS: Physical sciences

description: Employment outcomes of resettled refugees depend strongly on where they are placed inside the host country. Each week, a resettlement agency is assigned a batch of refugees by the United States government. The agency must place these refugees in its local affiliates, while respecting the affiliates' yearly capacities. We develop an allocation system that suggests where to place an incoming refugee, in order to improve total employment success. Our algorithm is based on two-stage stochastic programming and achieves over 98 percent of the hindsight-optimal employment, compared to under 90 percent of current greedy-like approaches. This dramatic improvement persists even when we incorporate a vast array of practical features of the refugee resettlement process including indivisible families, batching, and uncertainty with respect to the number of future arrivals. Our algorithm is now part of the Annie MOORE optimization software used by a leading American refugee resettlement agency.
description: Expanded related work, added experiments with bootstrapped arrivals in Section 7.2, added various experiments in the appendix
Acid stress response mechanisms of group B streptococci
Creators: name: Shabayek, Sarah
name: Spellerberg, Barbara
Publisher: name: Universität Ulm
Year: 2017
Subjects: subject: acid resistance
subject: low pH
subject: molecular mechanisms
subject: stress response
subject: DDC 610 / Medicine & health
subject: Streptococcus agalactiae
subject: Pregnancy complications, Infectious
subject: Communicable diseases; Transmission
subject: Schwangerschaft
subject: Krankheitsübertragung

description: Group B streptococcus (GBS) is a leading cause of neonatal mortality and morbidity in the United States and Europe. It is part of the vaginal microbiota in up to 30% of pregnant women and can be passed on to the newborn through perinatal transmission. GBS has the ability to survive in multiple different host niches. The pathophysiology of this bacterium reveals an outstanding ability to withstand varying pH fluctuations of the surrounding environments inside the human host. GBS host pathogen interations include colonization of the acidic vaginal mucosa, invasion of the neutral human blood or amniotic fluid, breaching of the blood brain barrier as well as survival within the acidic phagolysosomal compartment of macrophages. However, investigations on GBS responses to acid stress are limited. Technologies, such as whole genome sequencing, genome-wide transcription and proteome mapping facilitate large scale identification of genes and proteins. Mechanisms enabling GBS to cope with acid stress have mainly been studied through these techniques and are summarized in the current review
Trombiculindus Radford 1948
Creators: name: Nielsen, David H.
name: Robbins, Richard G.
name: Rueda, Leopoldo M.
Publisher: name: Zenodo
Year: 2021
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Arachnida
Actinedida
Trombiculidae
Trombiculindus

description: Trombiculindus Radford, 1948b
Trombiculindus Radford, 1948b; Kudryashova 1998
Trombiculindus (Plumosicola), Sinha 1954
Trombicula (Trombiculindus), Wharton & Fuller 1952; Sinha 1954
Leptotrombidium (Trombiculindus), Nadchatram & Dohany 1974
description: Published as part of Nielsen, David H., Robbins, Richard G. & Rueda, Leopoldo M., 2021, Annotated world checklist of the Trombiculidae and Leeuwenhoekiidae (1758 - 2021) (Acari: Trombiculoidea), with notes on nomenclature, taxonomy, and distribution, pp. 1-243 in Zootaxa 4967 (1) on page 186, DOI: 10.11646/zootaxa.4967.1.1, http://zenodo.org/record/4745510
Dictyonota astragali Stusak & Onder 1982
Creators: name: Dursun, Ahmet
name: Fent, Meral
Publisher: name: Zenodo
Year: 2017
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Hemiptera
Tingidae
Dictyonota
Dictyonota astragali

description: Dictyonota astragali Štusák & Önder, 1982
Material examined: ASIAN TURKEY: Amasya province: Merzifon, Çavundur, 463 m, 06.09.2016, 1♀. Asian Turkey: Štusák & Önder (1982), Lodos & Önder (1983), Péricart (1983), Péricart & Golub (1996), Önder et al. (2006), this study.
Comments: This species has been found under Astragalus sp. This finding is the second record of the species in Turkey. It has been described from Namrun Mountain (Bitlis province). It is a rare species represented only from the type locality and the present locality in Turkey. The features of this specimen were originally described by Štusák & Önder (1982) (Figs. 1a, b).
description: Published as part of Dursun, Ahmet & Fent, Meral, 2017, Annotated Checklist of Tingidae (Hemiptera: Heteroptera) in Turkey with new records for the faunas of Europe and Turkish Thrace, pp. 465-491 in Zootaxa 4347 (3) on page 475, DOI: 10.11646/zootaxa.4347.3.3, http://zenodo.org/record/1048601
Flexibility and regularity of the hydration structure of a sodium ion. Nonempirical insight
Creators: name: Novakovskaya, Yulia V.
Publisher: name: arXiv
Year: 2021
Subjects: subject: Chemical Physics (physics.chem-ph)
subject: Materials Science (cond-mat.mtrl-sci)
subject: Atomic and Molecular Clusters (physics.atm-clus)
subject: Computational Physics (physics.comp-ph)
subject: FOS: Physical sciences

description: The stationary nonempirical simulations of Na+(H2O)n clusters with n in a range of 28 to 51 carried out at the density functional level with a hybrid B3LYP functional and the Born-Oppenheimer molecular dynamics modeling of the size selected clusters reveal the interrelated structural and energetic peculiarities of sodium hydration structures. Surface, bulk, and transient configurations of the clusters are distinguished with the different location of the sodium nucleus (close to either the spatial center of the structure or one of its side faces) and its consistently changing coordination number (which typically equals five or six). The mean Na-O distances for the first-shell water molecules are found to depend both on the spatial character of the structure and the local coordination of sodium. The values are compared to different experimental estimates, and the virtual discrepancy of the latter is explained based on the results of the cluster simulations. Different coordination neighborhoods of sodium are predicted depending on its local fraction in the actual specimens.
Trombiculindus acanthosphenus Wang, Li and Shi 1988
Creators: name: Nielsen, David H.
name: Robbins, Richard G.
name: Rueda, Leopoldo M.
Publisher: name: Zenodo
Year: 2021
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Arachnida
Actinedida
Trombiculidae
Trombiculindus
Trombiculindus acanthosphenus

description: Trombiculindus acanthosphenus Wang, Li and Shi, 1988:
PAL
Trombiculindus (Trombiculindus) acanthosphenus Wang, Li and Shi, 1988
description: Published as part of Nielsen, David H., Robbins, Richard G. & Rueda, Leopoldo M., 2021, Annotated world checklist of the Trombiculidae and Leeuwenhoekiidae (1758 - 2021) (Acari: Trombiculoidea), with notes on nomenclature, taxonomy, and distribution, pp. 1-243 in Zootaxa 4967 (1) on page 186, DOI: 10.11646/zootaxa.4967.1.1, http://zenodo.org/record/4745510
A globally stable self-similar blowup profile in energy supercritical Yang-Mills theory
Creators: name: Donninger, Roland
name: Ostermann, Matthias
Publisher: name: arXiv
Year: 2021
Subjects: subject: Analysis of PDEs (math.AP)
subject: Mathematical Physics (math-ph)
subject: FOS: Mathematics
subject: FOS: Physical sciences

description: This paper is concerned with the Cauchy problem for an energy-supercritical nonlinear wave equation in odd space dimensions that arises in equivariant Yang-Mills theory. In each dimension, there is a self-similar finite-time blowup solution to this equation known in closed form. It will be proved that this profile is stable in the whole space under small perturbations of the initial data. The blowup analysis is based on a recently developed coordinate system called hyperboloidal similarity coordinates and depends crucially on growth estimates for the free wave evolution, which will be constructed systematically for odd space dimensions in the first part of this paper. This allows to develop a nonlinear stability theory beyond the singularity.
description: 57 pages, 5 figures, with minor improvements to match the published version
Pseudo-differential extension for graded nilpotent Lie groups
Creators: name: Ewert, Eske
Publisher: name: arXiv
Year: 2020
Subjects: subject: Operator Algebras (math.OA)
subject: FOS: Mathematics

description: Classical pseudo-differential operators of order zero on a graded nilpotent Lie group $G$ form a $^*$-subalgebra of the bounded operators on $L^2(G)$. We show that its $C^*$-closure is an extension of a noncommutative algebra of principal symbols by compact operators. As a new approach, we use the generalized fixed point algebra of an $\mathbb{R}_{>0}$-action on a certain ideal in the $C^*$-algebra of the tangent groupoid of $G$. The action takes the graded structure of $G$ into account. Our construction allows to compute the $K$-theory of the algebra of symbols.
description: 40 pages; parts of the paper were reorganized; Proposition 8.4 is a strengthening of result 10.5 in [V1], where only a bijection was shown
Dictyonota strichnocera Fieber 1844
Creators: name: Dursun, Ahmet
name: Fent, Meral
Publisher: name: Zenodo
Year: 2017
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Hemiptera
Tingidae
Dictyonota
Dictyonota strichnocera

description: Dictyonota strichnocera Fieber, 1844
Material examined: EUROPEAN TURKEY: Kırklareli province: Demirköy, Hamdibey, 130 m, 25.06.2015, 1♂.
Asian Turkey: Lodos & Önder (1983), Péricart (1983), Péricart & Golub (1996), Önder et al. (2006). European Turkey: This study. New record for the fauna of Turkish Thrace. Comments: In the study, this Mediterranean species has been recorded for the first time for the fauna of Turkish Thrace.
description: Published as part of Dursun, Ahmet & Fent, Meral, 2017, Annotated Checklist of Tingidae (Hemiptera: Heteroptera) in Turkey with new records for the faunas of Europe and Turkish Thrace, pp. 465-491 in Zootaxa 4347 (3) on page 476, DOI: 10.11646/zootaxa.4347.3.3, http://zenodo.org/record/1048601
Hybrid quantum-classical unsupervised data clustering based on the self-organizing feature map
Creators: name: Lazarev, Ilia D.
name: Narozniak, Marek
name: Byrnes, Tim
name: Pyrkov, Alexey N.
Publisher: name: arXiv
Year: 2020
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: Unsupervised machine learning is one of the main techniques employed in artificial intelligence. We introduce an algorithm for quantum-assisted unsupervised data clustering using the self-organizing feature map, a type of artificial neural network. The complexity of our algorithm scales as O(LN), in comparison to the classical case which scales as O(LMN), where N is the number of samples, M is the number of randomly sampled cluster vectors, and L is the number of the shifts of cluster vectors. We perform a proof-of-concept demonstration of one of the central components on the IBM quantum computer and show that it allows us to reduce the number of calculations in the number of clusters. Our algorithm exhibits exponential decrease in the errors of the distance matrix with the number of runs of the algorithm.
Robust and Efficient Estimation of Potential Outcome Means under Random Assignment
Creators: name: Negi, Akanksha
name: Wooldridge, Jeffrey M.
Publisher: name: arXiv
Year: 2020
Subjects: subject: Econometrics (econ.EM)
subject: FOS: Economics and business

description: We study efficiency improvements in randomized experiments for estimating a vector of potential outcome means using regression adjustment (RA) when there are more than two treatment levels. We show that linear RA which estimates separate slopes for each assignment level is never worse, asymptotically, than using the subsample averages. We also show that separate RA improves over pooled RA except in the obvious case where slope parameters in the linear projections are identical across the different assignment levels. We further characterize the class of nonlinear RA methods that preserve consistency of the potential outcome means despite arbitrary misspecification of the conditional mean functions. Finally, we apply these regression adjustment techniques to efficiently estimate the lower bound mean willingness to pay for an oil spill prevention program in California.
Probing nuclear structure with mean transverse momentum in relativistic isobar collisions
Creators: name: Xu, Hao-jie
name: Zhao, Wenbin
name: Li, Hanlin
name: Zhou, Ying
name: Chen, Lie-Wen
name: Wang, Fuqiang
Publisher: name: arXiv
Year: 2021
Subjects: subject: Nuclear Theory (nucl-th)
subject: Nuclear Experiment (nucl-ex)
subject: FOS: Physical sciences

description: Transverse momentum ($p_{T}$) generation in relativistic heavy ion collisions is sensitive to the initial geometry and the final-state bulk evolution. We demonstrate with hydrodynamic calculations that the mean $p_T$ ratio ($R_{\langle p_{T}\rangle}$) between the highly similar isobar $^{96}_{44}$Ru+$^{96}_{44}$Ru and $^{96}_{40}$Zr+$^{96}_{40}$Zr collisions is insensitive to the bulk evolution and remains sensitive to the small difference in the initial nuclear structure (neutron skin and deformation) between the Ru and Zr nuclei.We further find that nuclear deformation can produce an anticorrelation between $R_{\langle p_{T}\rangle}$ and eccentricity (or elliptic flow) in central collisions. These findings suggest that the $R_{\langle p_{T}\rangle}$ between the isobar systems can be used to measure the neutron skin thickness and deformation parameters, which can in turn constrain the nuclear symmetry energy slope parameter.
description: 6 pages, 5 figures
Polynomial XL: A Variant of the XL Algorithm Using Macaulay Matrices over Polynomial Rings
Creators: name: Furue, Hiroki
name: Kudo, Momonari
Publisher: name: arXiv
Year: 2021
Subjects: subject: Symbolic Computation (cs.SC)
subject: Cryptography and Security (cs.CR)
subject: Commutative Algebra (math.AC)
subject: FOS: Computer and information sciences
subject: FOS: Mathematics

description: Solving a system of $m$ multivariate quadratic equations in $n$ variables over finite fields (the MQ problem) is one of the important problems in the theory of computer science. The XL algorithm (XL for short) is a major approach for solving the MQ problem with linearization over a coefficient field. Furthermore, the hybrid approach with XL (h-XL) is a variant of XL guessing some variables beforehand. In this paper, we present a variant of h-XL, which we call the \textit{polynomial XL (PXL)}. In PXL, the whole $n$ variables are divided into $k$ variables to be fixed and the remaining $n-k$ variables as ``main variables'', and we generate a Macaulay matrix with respect to the $n-k$ main variables over a polynomial ring of the $k$ (sub-)variables. By eliminating some columns of the Macaulay matrix over the polynomial ring before guessing $k$ variables, the amount of operations required for each guessed value can be reduced compared with h-XL. Our complexity analysis of PXL (under some practical assumptions and heuristics) gives a new theoretical bound, and it indicates that PXL could be more efficient than other algorithms in theory on the random system with $n=m$, which is the case of general multivariate signatures. For example, on systems over the finite field with ${2^8}$ elements with $n=m=80$, the numbers of operations deduced from the theoretical bounds of the hybrid approaches with XL and Wiedemann XL, Crossbred, and PXL with optimal $k$ are estimated as $2^{252}$, $2^{234}$, $2^{237}$, and $2^{220}$, respectively.
description: 35 pages, 1 figure
Elasmotropis testacea subsp. testacea testacea (Herrich-Schaeffer 1830
Creators: name: Dursun, Ahmet
name: Fent, Meral
Publisher: name: Zenodo
Year: 2017
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Hemiptera
Tingidae
Elasmotropis
Elasmotropis testacea
Elasmotropis testacea testacea (herrich-Schaeffer, 1830)

description: Elasmotropis testacea testacea (Herrich-Schaeffer, 1830)
Material examined: ASIAN TURKEY: Erzincan province: Refahiye, Çavuşköy, 1571 m, 21.06.2007, 1♂; Gümüşhane province: Hasköy, 1176 m, 23.06.2007, 1♂; Köse, 493 m, 18.05.2006, 1♂; Köse-Öğünce, 1496 m, 18.05.2006, 2♀♀; Sivas province: Suşehri, Değirmentaş, 18.05.2006, 745 m, 1♂; Tokat province: Erbaa, Kaleköy, 210 m, 25.06.2005, 1♀; 07.08.2007, 1♂ Değirmenli, 210 m, 25.06.2006, 1♂.
Asian Turkey: Seidenstücker (1954), Hoberlandt (1956, as Elasmotropis testacea var. vicina), Linnavuori (1965), Lodos & Önder (1983), Péricart (1981a, 1983), Péricart & Golub (1996), Önder et al. (2006), Yıldırım et al. (2013), Matocq et al. (2014), Kıyak (2016), this study.
Comments: This species has been found for the first time from Erzurum by Yıldırım et al. (2013) and from Diyarbakır, Elazığ, Mardin by Matoq et al. (2014) as E. testacea selecta (Horváth, 1891) but Maral et al. (2014) reported from the same area (Diyarbakır, Elazığ, Mardin) as E. testacea testacea. Probably, Yıldırım et al. (2013) and Matoq et al. (2014) reported mistaken records. Matoq et al. (2014) reported that two subspecies as sympatric but did not provide any evidence of that. We believe that only nominotypical subspecies distributed in Turkey. This species has ben reported as an alien species by Kment (2006) and Rabitsch (2008).
description: Published as part of Dursun, Ahmet & Fent, Meral, 2017, Annotated Checklist of Tingidae (Hemiptera: Heteroptera) in Turkey with new records for the faunas of Europe and Turkish Thrace, pp. 465-491 in Zootaxa 4347 (3) on page 476, DOI: 10.11646/zootaxa.4347.3.3, http://zenodo.org/record/1048601
Hard and Soft EM in Bayesian Network Learning from Incomplete Data
Creators: name: Ruggieri, Andrea
name: Stranieri, Francesco
name: Stella, Fabio
name: Scutari, Marco
Publisher: name: arXiv
Year: 2020
Subjects: subject: Machine Learning (stat.ML)
subject: Machine Learning (cs.LG)
subject: Methodology (stat.ME)
subject: FOS: Computer and information sciences

description: Incomplete data are a common feature in many domains, from clinical trials to industrial applications. Bayesian networks (BNs) are often used in these domains because of their graphical and causal interpretations. BN parameter learning from incomplete data is usually implemented with the Expectation-Maximisation algorithm (EM), which computes the relevant sufficient statistics ("soft EM") using belief propagation. Similarly, the Structural Expectation-Maximisation algorithm (Structural EM) learns the network structure of the BN from those sufficient statistics using algorithms designed for complete data. However, practical implementations of parameter and structure learning often impute missing data ("hard EM") to compute sufficient statistics instead of using belief propagation, for both ease of implementation and computational speed. In this paper, we investigate the question: what is the impact of using imputation instead of belief propagation on the quality of the resulting BNs? From a simulation study using synthetic data and reference BNs, we find that it is possible to recommend one approach over the other in several scenarios based on the characteristics of the data. We then use this information to build a simple decision tree to guide practitioners in choosing the EM algorithm best suited to their problem.
description: 16 pages, 5 figures
Trombiculindus aetheruis Fernandes and Kulkarni 2003
Creators: name: Nielsen, David H.
name: Robbins, Richard G.
name: Rueda, Leopoldo M.
Publisher: name: Zenodo
Year: 2021
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Arachnida
Actinedida
Trombiculidae
Trombiculindus
Trombiculindus aetheruis

description: Trombiculindus aetheruis Fernandes and Kulkarni, 2003:
PAL
description: Published as part of Nielsen, David H., Robbins, Richard G. & Rueda, Leopoldo M., 2021, Annotated world checklist of the Trombiculidae and Leeuwenhoekiidae (1758 - 2021) (Acari: Trombiculoidea), with notes on nomenclature, taxonomy, and distribution, pp. 1-243 in Zootaxa 4967 (1) on page 186, DOI: 10.11646/zootaxa.4967.1.1, http://zenodo.org/record/4745510
Positive oriented Thompson links
Creators: name: Aiello, Valeriano
name: Baader, Sebastian
Publisher: name: arXiv
Year: 2021
Subjects: subject: Geometric Topology (math.GT)
subject: Group Theory (math.GR)
subject: Operator Algebras (math.OA)
subject: FOS: Mathematics

description: We prove that the links associated with positive elements of the oriented subgroup of the Thompson group are positive.
description: Accepted for publication in Communications in Analysis and Geometry
Optically excited spin dynamics of thermally metastable skyrmions in Fe$_{0.75}$Co$_{0.25}$Si
Creators: name: Kalin, Jantje
name: Sievers, Sibylle
name: Füser, Heiko
name: Schumacher, Hans Werner
name: García-Sánchez, Felipe
name: Bauer, Andreas
name: Pfleiderer, Christian
name: Bieler, Mark
Publisher: name: arXiv
Year: 2022
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Applied Physics (physics.app-ph)
subject: FOS: Physical sciences

description: We investigate the microwave spin excitations of the cubic chiral magnet Fe$_{0.75}$Co$_{0.25}$Si as driven by the thermal modulation of magnetic interactions via laser heating and probed by time-resolved measurements of the magneto-optical Kerr effect. Focusing on the topologically nontrivial skyrmion lattice state, the dynamic properties in thermodynamic equilibrium are compared with those of a metastable state prepared by means of rapid field cooling. In both cases, we find precessional and exponential contributions to the dynamic response, characteristic of a breathing mode and energy dissipation, respectively. When taking into account the universal scaling as a function of temperature, the precession frequencies in the equilibrium and metastable skyrmion state are in excellent quantitative agreement. This finding highlights that skyrmion states far from thermal equilibrium promise great flexibility, for instance with respect to temperature and field scales, both for possible microwave applications and the study of fundamental properties.
description: 16 pages, 4 figures
Reasoning with fuzzy and uncertain evidence using epistemic random fuzzy sets: general framework and practical models
Creators: name: Denoeux, Thierry
Publisher: name: arXiv
Year: 2022
Subjects: subject: Artificial Intelligence (cs.AI)
subject: Methodology (stat.ME)
subject: FOS: Computer and information sciences

description: We introduce a general theory of epistemic random fuzzy sets for reasoning with fuzzy or crisp evidence. This framework generalizes both the Dempster-Shafer theory of belief functions, and possibility theory. Independent epistemic random fuzzy sets are combined by the generalized product-intersection rule, which extends both Dempster's rule for combining belief functions, and the product conjunctive combination of possibility distributions. We introduce Gaussian random fuzzy numbers and their multi-dimensional extensions, Gaussian random fuzzy vectors, as practical models for quantifying uncertainty about scalar or vector quantities. Closed-form expressions for the combination, projection and vacuous extension of Gaussian random fuzzy numbers and vectors are derived.
Galeatus cellularis Jakovlev 1884
Creators: name: Dursun, Ahmet
name: Fent, Meral
Publisher: name: Zenodo
Year: 2017
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Hemiptera
Tingidae
Galeatus
Galeatus cellularis

description: Galeatus cellularis Jakovlev, 1884
Asian Turkey: Seidenstücker (1957, as Calcatus cellularis), Lodos & Önder (1983), Péricart (1983), Péricart & Golub (1996), Önder et al. (2006).
description: Published as part of Dursun, Ahmet & Fent, Meral, 2017, Annotated Checklist of Tingidae (Hemiptera: Heteroptera) in Turkey with new records for the faunas of Europe and Turkish Thrace, pp. 465-491 in Zootaxa 4347 (3) on page 476, DOI: 10.11646/zootaxa.4347.3.3, http://zenodo.org/record/1048601
Limitations to photosynthesis in bryophytes: certainties and uncertainties regarding methodology
Creators: name: Perera-Castro, AV
name: Waterman, Melinda
name: Robinson, Sharon
name: Flexas, J
Publisher: name: University of Wollongong
Year: 2024
Subjects: classificationCode: 31
subject: Biological sciences
subject: FOS: Biological sciences
classificationCode: 3101
subject: Biochemistry and cell biology
classificationCode: 3004
subject: Crop and pasture production
classificationCode: 3108
subject: Plant biology
classificationCode: 3105
subject: Genetics

description: Bryophytes are the group of land plants with the lowest photosynthetic rates, which was considered to be a consequence of their higher anatomical CO2 diffusional limitation compared with tracheophytes. However, the most recent studies assessing limitations due to biochemistry and mesophyll conductance in bryophytes reveal discrepancies based on the methodology used. In this study, we compared data calculated from two different methodologies for estimating mesophyll conductance: variable J and the curve-fitting method. Although correlated, mesophyll conductance estimated by the curve-fitting method was on average 4-fold higher than the conductance obtained by the variable J method; a large enough difference to account for the scale of differences previously shown between the biochemical and diffusional limitations to photosynthesis. Biochemical limitations were predominant when the curve-fitting method was used. We also demonstrated that variations in bryophyte relative water content during measurements can also introduce errors in the estimation of mesophyll conductance, especially for samples which are overly desiccated. Furthermore, total chlorophyll concentration and soluble proteins were significantly lower in bryophytes than in tracheophytes, and the percentage of proteins quantified as Rubisco was also significantly lower in bryophytes (<6.3% in all studied species) than in angiosperms (>16% in all non-stressed cases). Photosynthetic rates normalized by Rubisco were not significantly different between bryophytes and angiosperms. Our data suggest that the biochemical limitation to photosynthesis in bryophytes is more relevant than so far assumed.
Trombiculindus alethrix , Stekolnikov 2021
Creators: name: Nielsen, David H.
name: Robbins, Richard G.
name: Rueda, Leopoldo M.
Publisher: name: Zenodo
Year: 2021
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Arachnida
Actinedida
Trombiculidae
Trombiculindus
Trombiculindus alethrix

description: Trombiculindus alethrix (Traub and Nadchatram, 1967a):
ORI
Leptotrombidium (Trombiculindus) alethrix Traub and Nadchatram, 1967 a
Trombiculindus alethrix, Stekolnikov 2021
description: Published as part of Nielsen, David H., Robbins, Richard G. & Rueda, Leopoldo M., 2021, Annotated world checklist of the Trombiculidae and Leeuwenhoekiidae (1758 - 2021) (Acari: Trombiculoidea), with notes on nomenclature, taxonomy, and distribution, pp. 1-243 in Zootaxa 4967 (1) on page 186, DOI: 10.11646/zootaxa.4967.1.1, http://zenodo.org/record/4745510
Dorsal raphe nucleus down-regulates medial prefrontal cortex during experience of flow
Creators: name: Ulrich, Martin
name: Keller, Johannes
name: Grön, Georg
Publisher: name: Universität Ulm
Year: 2016
Subjects: subject: flow experience
subject: dynamic causal modeling
subject: effective connectivity
subject: medial prefrontal cortex
subject: midbrain
subject: functional magnetic resonance imaging
subject: DDC 610 / Medicine & health
subject: Dorsal raphe nucleus
subject: Prefrontal cortex
subject: Amygdala
subject: Magnetic resonance imaging
subject: Funktionelle Kernspintomografie
subject: Modellierung
subject: Präfrontaler Cortex

description: Previous neuroimaging studies have suggested that the experience of flow aligns with a relative increase in activation of the dorsal raphe nucleus (DRN), and relative activation decreases of the medial prefrontal cortex (MPFC) and of the amygdala (AMY). In the present study, Dynamic Causal Modeling (DCM) was used to explore effective connectivity between those brain regions. To test our hypothesis that the DRN causally down-regulates activity of the MPFC and/or of the AMY, 23 healthy male students solved mental arithmetic tasks of varying difficulty during functional magnetic resonance imaging. A “flow” condition, with task demands automatically balanced with participants’ skill level, was compared with conditions of “boredom” and “overload”. DCM models were constructed modeling full reciprocal endogenous connections between the DRN, the MPFC, the AMY, and the calcarine. The calcarine was included to allow sensory input to enter the system. Experimental conditions were modeled as exerting modulatory effects on various possible connections between the DRN, the MPFC, and the AMY, but not on self-inhibitory connections, yielding a total of 64 alternative DCM models. Model space was partitioned into eight families based on commonalities in the arrangement of the modulatory effects. Random effects Bayesian Model Selection (BMS) was applied to identify a possible winning family (and model). Although BMS revealed a clear winning family, an outstanding winning model could not be identified. Therefore, Bayesian Model Averaging was performed over models within the winning family to obtain representative DCM parameters for subsequent analyses to test our hypothesis. In line with our expectations, Bayesian averaged parameters revealed stronger down-regulatory influence of the DRN on the MPFC when participants experienced flow relative to control conditions. In addition, these condition-dependent modulatory effects significantly predicted participants’ experienced degree of flow. The AMY was down-regulated irrespective of condition. The present results suggest a causal role for the DRN in modulating the MPFC, contributing to the experience of flow.
Newton polytope of good symmetric polynomials
Creators: name: Duc, Khanh Nguyen
name: Giao, Nguyen Thi Ngoc
name: Hiep, Dang Tuan
name: Thuy, Do Le Hai
Publisher: name: arXiv
Year: 2022
Subjects: subject: Combinatorics (math.CO)
subject: Algebraic Geometry (math.AG)
subject: Representation Theory (math.RT)
subject: FOS: Mathematics
subject: 52B20, 05E05

description: We introduce a general class of symmetric polynomials that have saturated Newton polytope and their Newton polytope has integer decomposition property. The class covers numerous previously studied symmetric polynomials.
description: 10 pages, 3 figures
Galeatus scrophicus Saunders 1876
Creators: name: Dursun, Ahmet
name: Fent, Meral
Publisher: name: Zenodo
Year: 2017
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Hemiptera
Tingidae
Galeatus
Galeatus scrophicus

description: Galeatus scrophicus Saunders, 1876
Asian Turkey: Hoberlandt (1956), Önder & Lodos (1977), Kıran (1978), Lodos & Önder (1983), Péricart (1983), Péricart & Golub (1996), Önder et al. (2006), Maral et al. (2013).
Comments: This cosmopolitan species has been found for the first time in Turkey at Kızıltepe (Mardin) and Şanlıurfa on sunflower by Önder & Lodos (1977) and described as Galeatus helianthi. It is distributed in Asia, Europe, North Africa, South Africa and India (Deckert & Göllner-Scheiding 2006).
description: Published as part of Dursun, Ahmet & Fent, Meral, 2017, Annotated Checklist of Tingidae (Hemiptera: Heteroptera) in Turkey with new records for the faunas of Europe and Turkish Thrace, pp. 465-491 in Zootaxa 4347 (3) on page 476, DOI: 10.11646/zootaxa.4347.3.3, http://zenodo.org/record/1048601
Multipole Born series approach to light scattering by Mie-resonant nanoparticle structures
Creators: name: Ustimenko, Nikita A.
name: Kornovan, Danil F.
name: Baryshnikova, Kseniia V.
name: Evlyukhin, Andrey B.
name: Petrov, Mihail I.
Publisher: name: arXiv
Year: 2021
Subjects: subject: Optics (physics.optics)
subject: FOS: Physical sciences

description: Exciting optical effects such as polarization control, imaging, and holography were demonstrated at the nanoscale using the complex and irregular structures of nanoparticles with the multipole Mie-resonances in the optical range. The optical response of such particles can be simulated either by full wave numerical simulations or by the widely used analytical coupled multipole method (CMM), however, an analytical solution in the framework of CMM can be obtained only in a limited number of cases. In this paper, a modification of the CMM in the framework of the Born series and its applicability for simulation of light scattering by finite nanosphere structures, maintaining both dipole and quadrupole resonances, are investigated. The Born approximation simplifies an analytical consideration of various systems and helps shed light on physical processes ongoing in that systems. Using Mie theory and Green's functions approach, we analytically formulate the rigorous coupled dipole-quadrupole equations and their solution in the different-order Born approximations. We analyze in detail the resonant scattering by dielectric nanosphere structures such as dimer and ring to obtain the convergence conditions of the Born series and investigate how the physical characteristics such as absorption in particles, type of multipole resonance, and geometry of ensemble influence the convergence of Born series and its accuracy.
Trombiculindus alpinus Yu and Yang 1979
Creators: name: Nielsen, David H.
name: Robbins, Richard G.
name: Rueda, Leopoldo M.
Publisher: name: Zenodo
Year: 2021
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Arachnida
Actinedida
Trombiculidae
Trombiculindus
Trombiculindus alpinus

description: Trombiculindus alpinus Yu and Yang, 1979:
PAL
Trombiculindus (Trombiculindus) alpinus Yu and Yang, 1979
description: Published as part of Nielsen, David H., Robbins, Richard G. & Rueda, Leopoldo M., 2021, Annotated world checklist of the Trombiculidae and Leeuwenhoekiidae (1758 - 2021) (Acari: Trombiculoidea), with notes on nomenclature, taxonomy, and distribution, pp. 1-243 in Zootaxa 4967 (1) on page 186, DOI: 10.11646/zootaxa.4967.1.1, http://zenodo.org/record/4745510
Pseudodifferential operators on filtered manifolds as generalized fixed points
Creators: name: Ewert, Eske
Publisher: name: arXiv
Year: 2021
Subjects: subject: Operator Algebras (math.OA)
subject: Differential Geometry (math.DG)
subject: FOS: Mathematics

description: On filtered manifolds one can define a different notion of order for the differential operators. In this paper, we use generalized fixed point algebras to construct a pseudodifferential extension that reflects this behaviour. In the corresponding calculus, the principal symbol of an operator is a family of operators acting on certain nilpotent Lie groups. The role of ellipticity as a Fredholm condition is replaced by the Rockland condition on these groups. Our approach allows to understand this in terms of the representation of the corresponding algebra of principal symbols. Moreover, we compute the $K$-theory of this algebra.
description: 37 pages
Trombiculindus armatus
Creators: name: Nielsen, David H.
name: Robbins, Richard G.
name: Rueda, Leopoldo M.
Publisher: name: Zenodo
Year: 2021
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Arachnida
Actinedida
Trombiculidae
Trombiculindus
Trombiculindus armatus

description: Trombiculindus armatus (Traub, Nadchatram and Lakshana, 1968):
ORI
Leptotrombidium (Trombiculindus) armatum Traub, Nadchatram and Lakshana, 1968
Trombiculindus armatum, Chaisiri et al. 2016; Stekolnikov 2021
description: Published as part of Nielsen, David H., Robbins, Richard G. & Rueda, Leopoldo M., 2021, Annotated world checklist of the Trombiculidae and Leeuwenhoekiidae (1758 - 2021) (Acari: Trombiculoidea), with notes on nomenclature, taxonomy, and distribution, pp. 1-243 in Zootaxa 4967 (1) on page 186, DOI: 10.11646/zootaxa.4967.1.1, http://zenodo.org/record/4745510
Topology of the O(3) non-linear sigma model under the gradient flow
Creators: name: Yi-Thomas, Stuart
name: Monahan, Christopher
Publisher: name: arXiv
Year: 2021
Subjects: subject: High Energy Physics - Lattice (hep-lat)
subject: FOS: Physical sciences

description: The O(3) non-linear sigma model (NLSM) is a prototypical field theory for QCD and ferromagnetism, and provides a simple system in which to study topological effects. In lattice QCD, the gradient flow has been demonstrated to remove ultraviolet singularities from the topological susceptibility. In contrast, lattice simulations of the NLSM find that the topological susceptibility diverges in the continuum limit, even in the presence of the gradient flow. We introduce a $θ$-term and analyze the topological charge as a function of $θ$ under the gradient flow. Our results show that divergence persists in the presence of the flow, even at non-zero $θ$.
description: The 38th International Symposium on Lattice Field Theory, LATTICE2021 26th-30th July, 2021 Zoom/Gather@Massachusetts Institute of Technology
LordNet: An Efficient Neural Network for Learning to Solve Parametric Partial Differential Equations without Simulated Data
Creators: name: Huang, Xinquan
name: Shi, Wenlei
name: Gao, Xiaotian
name: Wei, Xinran
name: Zhang, Jia
name: Bian, Jiang
name: Yang, Mao
name: Liu, Tie-Yan
Publisher: name: arXiv
Year: 2022
Subjects: subject: Machine Learning (cs.LG)
subject: FOS: Computer and information sciences

description: Neural operators, as a powerful approximation to the non-linear operators between infinite-dimensional function spaces, have proved to be promising in accelerating the solution of partial differential equations (PDE). However, it requires a large amount of simulated data, which can be costly to collect. This can be avoided by learning physics from the physics-constrained loss, which we refer to it as mean squared residual (MSR) loss constructed by the discretized PDE. We investigate the physical information in the MSR loss, which we called long-range entanglements, and identify the challenge that the neural network requires the capacity to model the long-range entanglements in the spatial domain of the PDE, whose patterns vary in different PDEs. To tackle the challenge, we propose LordNet, a tunable and efficient neural network for modeling various entanglements. Inspired by the traditional solvers, LordNet models the long-range entanglements with a series of matrix multiplications, which can be seen as the low-rank approximation to the general fully-connected layers and extracts the dominant pattern with reduced computational cost. The experiments on solving Poisson's equation and (2D and 3D) Navier-Stokes equation demonstrate that the long-range entanglements from the MSR loss can be well modeled by the LordNet, yielding better accuracy and generalization ability than other neural networks. The results show that the Lordnet can be $40\times$ faster than traditional PDE solvers. In addition, LordNet outperforms other modern neural network architectures in accuracy and efficiency with the smallest parameter size.
Lee classes on LCK manifolds with potential
Creators: name: Ornea, Liviu
name: Verbitsky, Misha
Publisher: name: arXiv
Year: 2021
Subjects: subject: Differential Geometry (math.DG)
subject: Algebraic Geometry (math.AG)
subject: FOS: Mathematics
subject: 53C55, 32G05

description: An LCK (locally conformally Kahler) manifold is a complex manifold $(M,I)$ equipped with a Hermitian form $ω$ and a closed 1-form $θ$, called the Lee form, such that $dω=θ\wedgeω$. An LCK manifold with potential is an LCK manifold with a positive Kahler potential on its cover, such that the deck group multiplies the Kahler potential by a constant. A Lee class of an LCK manifold is the cohomology class of the Lee form. We determine the set of Lee classes on LCK manifolds admitting an LCK structure with potential, showing that it is an open half-space in $H^1(M,{\mathbb R})$. For Vaisman manifolds, this theorem was proven in 1994 by Tsukada; we give a new self-contained proof of his result.
description: 27 pages, version 2.0, minor errors corrected
Autonomous scanning probe microscopy with hypothesis learning: Exploring the physics of domain switching in ferroelectric materials
Creators: name: Liu, Yongtao
name: Morozovska, Anna
name: Eliseev, Eugene
name: Kelley, Kyle P.
name: Vasudevan, Rama
name: Ziatdinov, Maxim
name: Kalinin, Sergei V.
Publisher: name: arXiv
Year: 2022
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: We report the development and implementation of a hypothesis learning based automated experiment, in which the microscope operating in the autonomous mode identifies the physical laws behind the material's response. Specifically, we explore the bias induced transformations that underpin the functionality of broad classes of devices and functional materials from batteries and memristors to ferroelectrics and antiferroelectrics. Optimization and design of these materials require probing the mechanisms of these transformations on the nanometer scale as a function of the broad range of control parameters such as applied potential and time, often leading to experimentally intractable scenarios. At the same time, often the behaviors of these systems are understood within potentially competing theoretical models, or hypotheses. Here, we develop a hypothesis list that covers the possible limiting scenarios for the domain growth, including thermodynamic, domain wall pinning, and screening limited. We further develop and experimentally implement the hypothesis driven automated experiment in Piezoresponse Force Microscopy, autonomously identifying the mechanisms of the bias induced domain switching. This approach can be applied for a broad range of physical and chemical experiments with relatively low dimensional control parameter space and for which the possible competing models of the system behavior that ideally cover the full range of physical eventualities are known or can be created. These include other scanning probe microscopy modalities such as force distance curve measurements and nanoindentation, as well as materials synthesis and optimization.
description: 25 pages, 6 figures
Kalama lugubris
Creators: name: Dursun, Ahmet
name: Fent, Meral
Publisher: name: Zenodo
Year: 2017
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Hemiptera
Tingidae
Kalama
Kalama lugubris

description: Kalama lugubris (Fieber, 1861)
Material examined: EUROPEAN TURKEY: Edirne province: Meriç, Olacak, 140 m, 18.05.2016, 3♀♀, 2♂♂; Kadıdondurma, 18.05.2016, 1♀, 1♂; Uzunköprü, 160 m, 14.07.2016, 1♂; Paşayiğit, 80 m, 20.07.2016, 1♂.
Asian Turkey: Péricart (1983), Péricart & Golub (1996), Matoq et al. (2014).
European Turkey: Lodos & Önder (1983, as Dictyonata lugubris), Péricart (1983); Péricart & Golub (1996), Önder et al. (2006, as D. lugubris), this study. First exact records from Turkish Thrace.
Comments: This Eastmediterranean species was recorded from Istanbul as Dictyonota lugubris (Fieber, 1861) by Lodos & Önder (1983). However, since Istanbul is represented both in Anatolia and Thrace regions, the finding of Lodos & Önder (1983) is not clearly related with Thrace region. We report here the first exact locality (Kadıdondurma, Edirne province) from Turkish Thrace.
description: Published as part of Dursun, Ahmet & Fent, Meral, 2017, Annotated Checklist of Tingidae (Hemiptera: Heteroptera) in Turkey with new records for the faunas of Europe and Turkish Thrace, pp. 465-491 in Zootaxa 4347 (3) on page 477, DOI: 10.11646/zootaxa.4347.3.3, http://zenodo.org/record/1048601