cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Formal Foundations for Translational Separation Logic Verifiers (extended version)
Creators: name: Dardinier, Thibault
name: Sammler, Michael
name: Parthasarathy, Gaurav
name: Summers, Alexander J.
name: Müller, Peter
Publisher: name: arXiv
Year: 2024
Subjects: subject: Programming Languages (cs.PL)
subject: FOS: Computer and information sciences

description: Program verification tools are often implemented as front-end translations of an input program into an intermediate verification language (IVL) such as Boogie, GIL, Viper, or Why3. The resulting IVL program is then verified using an existing back-end verifier. A soundness proof for such a translational verifier needs to relate the input program and verification logic to the semantics of the IVL, which in turn needs to be connected with the verification logic implemented in the back-end verifiers. Performing such proofs is challenging due to the large semantic gap between the input and output programs and logics, especially for complex verification logics such as separation logic.
 This paper presents a formal framework for reasoning about translational separation logic verifiers. At its center is a generic core IVL that captures the essence of different separation logics. We define its operational semantics and formally connect it to two different back-end verifiers, which use symbolic execution and verification condition generation, resp. Crucially, this semantics uses angelic non-determinism to enable the application of different proof search algorithms and heuristics in the back-end verifiers. An axiomatic semantics for the core IVL simplifies reasoning about the front-end translation by performing essential proof steps once and for all in the equivalence proof with the operational semantics rather than for each concrete front-end translation.
 We illustrate the usefulness of our formal framework by instantiating our core IVL with elements of Viper and connecting it to two Viper back-ends as well as a front-end for concurrent separation logic. All our technical results have been formalized in Isabelle/HOL, including the core IVL and its semantics, the semantics of two back-ends for a subset of Viper, and all proofs.
description: Extended version of POPL'25 paper
Additional file 18: Table S16. of Exploring the rice dispensable genome using a metagenome-like assembly strategy
Creators: name: Yao, Wen
name: Guangwei Li
name: Zhao, Hu
name: Gongwei Wang
name: Xingming Lian
name: Weibo Xie
Publisher: name: Figshare
Year: 2015
Subjects: subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Evolutionary Biology
subject: Sociology
subject: FOS: Sociology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Ecology
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Marine Biology
subject: Cancer
subject: 110309 Infectious Diseases
subject: FOS: Health sciences

description: Functional enrichment analysis of 6302 reference genes involved in the formation of non-reference sequences through exon/intron shuffling. The hmm accession for all the 6302 reference genes was extracted, and the number of genes with a specific hmm accession involved in the formation of non-reference sequences through exon/intron shuffling were compared with the whole genome level to find enriched accessions. In total, 3581 of these 6302 genes and 33,581 genes of the whole genome were annotated by Pfam. (DOC 40Â kb)
Synthetic Simplicity: Unveiling Bias in Medical Data Augmentation
Creators: name: Babu, Krishan Agyakari Raja
name: Sathish, Rachana
name: Pattanaik, Mrunal
name: Venkataramani, Rahul
Publisher: name: arXiv
Year: 2024
Subjects: subject: Computer Vision and Pattern Recognition (cs.CV)
subject: Artificial Intelligence (cs.AI)
subject: FOS: Computer and information sciences

description: Synthetic data is becoming increasingly integral in data-scarce fields such as medical imaging, serving as a substitute for real data. However, its inherent statistical characteristics can significantly impact downstream tasks, potentially compromising deployment performance. In this study, we empirically investigate this issue and uncover a critical phenomenon: downstream neural networks often exploit spurious distinctions between real and synthetic data when there is a strong correlation between the data source and the task label. This exploitation manifests as \textit{simplicity bias}, where models overly rely on superficial features rather than genuine task-related complexities. Through principled experiments, we demonstrate that the source of data (real vs.\ synthetic) can introduce spurious correlating factors leading to poor performance during deployment when the correlation is absent. We first demonstrate this vulnerability on a digit classification task, where the model spuriously utilizes the source of data instead of the digit to provide an inference. We provide further evidence of this phenomenon in a medical imaging problem related to cardiac view classification in echocardiograms, particularly distinguishing between 2-chamber and 4-chamber views. Given the increasing role of utilizing synthetic datasets, we hope that our experiments serve as effective guidelines for the utilization of synthetic datasets in model training.
Additional file 1: Table S1. of Exploring the rice dispensable genome using a metagenome-like assembly strategy
Creators: name: Yao, Wen
name: Guangwei Li
name: Zhao, Hu
name: Gongwei Wang
name: Xingming Lian
name: Weibo Xie
Publisher: name: Figshare
Year: 2015
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Evolutionary Biology
subject: Ecology
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Marine Biology

description: Collection of sequence data. (DOCX 14Â kb)
Gaertnera luteocarpa subsp. luteocarpa
Creators: name: Jongkind, Carel Christiaan Hugo
Publisher: name: Zenodo
Year: 2015
Subjects: Biodiversity
Taxonomy
Plantae
Tracheophyta
Magnoliopsida
Gentianales
Rubiaceae
Gaertnera
Gaertnera luteocarpa
Gaertnera luteocarpa jongkind subsp. luteocarpa

description: Gaertnera luteocarpa Jongkind subsp. luteocarpa
(Figs 1, 4)
Diagnostic characters
Fertile branches twice the size of the other subspecies (4 mm wide in dry state). Stipular tube densely pale hairy.
Distribution
Undergrowth of evergreen lowland forest often on swampy places. South-west Ghana and south Ivory Coast.
Additional specimens studied
GHANA. Western Region, Ankasa River Forest Reserve, fr., 4 Jan. 1969, Enti & Hall GC 39103 (GC n.v., K); ibid., young fr., 29 Dec. 1966, Hall & Enti GC 36155 (K); ibid., young fr., 12 Nov. 1967, Hall GC 37121 (K); Ankasa River Reserve, 24 Apr. 2001, Hawthorne & Gyakari 201a223 (FHO); ibid., 3 Mar. 2003, Hawthorne & Gyakari 203a123 (FHO); ibid., 28 Feb. 2005, Hawthorne & Gyakari 205a063 (FHO); near Ankasa Game Reserve, fr., 28 Feb. 1995, Jongkind, Abbiw & Markwei 2077 (MO, WAG)
Conservation status
The EOO is 1398 km 2 and the AOO is 20 km 2, both count as “Endangered”. The AOO is based on a cell width of 2 km. This calculation of the EOO as one continuous area is much too high looking at the big gap between the most western occurrence and all other ones. Most specimens were collected in the Ankasa Reserve and that is the only forest area where this subspecies is found more than once. Most forests connecting the two locations of the subspecies has disappeared in recent years. Like for the species itself I propose “Endangered” for this subspecies (B1 & B2 ab(iii) IUCN 2015).
Remark
The holotype of G. luteocarpa sp. nov. was not recognized before as a Gaertnera species and for years misplaced in the herbarium as Bertiera racemosa (G.Don) K.Schum.
description: Published as part of Jongkind, Carel Christiaan Hugo, 2015, Description of Gaertnera luteocarpa (Gentianales: Rubiaceae), with two subspecies, a new forest shrub species from Liberia, Ivory Coast and Ghana, pp. 1-8 in European Journal of Taxonomy 126 on page 5, DOI: 10.5852/ejt.2015.126, http://zenodo.org/record/3780350
Additional file 7: Table S6. of Exploring the rice dispensable genome using a metagenome-like assembly strategy
Creators: name: Yao, Wen
name: Guangwei Li
name: Zhao, Hu
name: Gongwei Wang
name: Xingming Lian
name: Weibo Xie
Publisher: name: Figshare
Year: 2015
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Evolutionary Biology
subject: Ecology
subject: 69999 Biological Sciences not elsewhere classified
subject: Marine Biology

description: Blastn alignment result of the full-length cDNA sequences of 12 O. rufipogon genes to the contigs of the dispensable genome. (DOC 35Â kb)
Sound Speed Resonance of Gravitational Waves in Gauss-Bonnet-coupled inflation
Creators: name: Addazi, Andrea
name: Aldabergenov, Yermek
name: Cai, Yifu
Publisher: name: arXiv
Year: 2024
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: We demonstrate the occurrence of Sound Speed Resonances (SSR) in Gauss-Bonnet-coupled inflation across a wide range of coupling functions and parameters. After inflation, the damped oscillations of the inflaton around its potential minimum induces damped oscillations of the sound speed of tensor modes, leading to resonant amplification of the latter. Once the inflaton stabilizes around the minimum, the tensor sound speed reduces to unity (speed of light). In the context of multi-field inflation, the sound speed oscillations can be followed by a second phase of inflation, resulting in a distinctive stochastic background of Gravitational Waves (GWs). We show that these GW signals can be probed by upcoming experiments such as $\textbf{SKA}$, $\textbf{DECIGO}$, and $\textbf{BBO}$ depending on the duration of the second inflationary phase.
description: 9 pages, 4 figures. V.2: revised version accepted to PRD
Additional file 2: Table S1. of Genome-wide analysis, molecular cloning and expression profiling reveal tissue-specifically expressed, feedback-regulated, stress-responsive and alternatively spliced novel genes involved in gibberellin metabolism in Salvia miltiorrhiza
Creators: name: Du, Qing
name: Caili Li
name: Dongqiao Li
name: Shanfa Lu
Publisher: name: Figshare
Year: 2015
Subjects: subject: Biochemistry
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Physiology
subject: Biotechnology
subject: Evolutionary Biology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: Developmental Biology
subject: Cancer
subject: Inorganic Chemistry
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: 60506 Virology
subject: Computational Biology

description: Sequence features of gibberellin metabolism genes in A. thaliana. The accession numbers, cDNA length, number of amino acid residues, molecular weight, pI and predicted protein localization are shown. (DOC 59 kb)
title: Hohe Nationalversammlung! Der unglückselige Aufstand, den der Beschluß der Nationalversammlung in Betreff des Malmöer Waffenstillstandes veranlaßt hat, und in welchem das deutsche Volk ein verbrecherisches Attentat gegen die Freiheit und Unverletzlichkeit der Träger seiner Souveränetät [!] tief beklagen muß, ...; [1848]
title: [Breslau, den 1. October 1848]
titleType: Subtitle
Creators: name: Dyrenfurth, ...
name: Borchardt, ...
Publisher: name: Universitätsbibliothek der Ludwig-Maximilians-Universität München
Year: 2018

description: Provenienz: Schauss, Anton | Einband = 0014/W 2 Hist. 2558
description: Kopftitel
Gaertnera luteocarpa subsp. sinoensis Jongkind 2015, subsp. nov.
Creators: name: Jongkind, Carel Christiaan Hugo
Publisher: name: Zenodo
Year: 2015
Subjects: Biodiversity
Taxonomy
Plantae
Tracheophyta
Magnoliopsida
Gentianales
Rubiaceae
Gaertnera
Gaertnera luteocarpa
Gaertnera luteocarpa jongkind subsp. sinoensis jongkind

description: Gaertnera luteocarpa Jongkind subsp. sinoensis Jongkind subsp. nov.urn:lsid:ipni.org:names:77147377-1 (Figs 2, 4)
Diagnosis
Fertile branches half the size as of the other subspecies (2 mm wide in dry state). Stipular tube glabrous, not densely hairy.
Type
LIBERIA. Sino County, Sapo National Park not far from Camp 6, 5°18.5’ N, 8°44.8’ W, alt: 220 m, fr., 22 Nov. 2010, Jongkind, Bilivogui & Daniels 9832 (holo-: WAG, iso-: BR).
Etymology
The subspecies is named after “ Sinoe ”, the river close to which it was seen for the first time.
Distribution and habitat
Known only from the south-east of Liberia.
Additional specimens examined
LIBERIA. Sino County, SSW of Jalay’s Town near the Sinoe River, 5°20’ N, 8°49’ W, alt: 90–100 m, fl. bud, 10 Mar. 2009, Jongkind, Bilivogui & Dorbor 8923 (WAG); c. 50 km east of Greenville, 5°04.61’ N, 8°30.42’ W, alt: 59 m, fl., 18 Mar. 2014, Jongkind & Mulbah 12500 (BR, K, MO).
Conservation status
The EOO is 54 km 2 and the AOO is 12 km 2, both count as “Endangered”. The AOO is based on a cell width of 2 km. Only one of the specimens was collected in a protected area. Considering all the economical development planned in this part of Liberia, I propose “Endangered” for this subspecies (B1 & B2 ab(iii) IUCN 2015).
description: Published as part of Jongkind, Carel Christiaan Hugo, 2015, Description of Gaertnera luteocarpa (Gentianales: Rubiaceae), with two subspecies, a new forest shrub species from Liberia, Ivory Coast and Ghana, pp. 1-8 in European Journal of Taxonomy 126 on pages 5-7, DOI: 10.5852/ejt.2015.126, http://zenodo.org/record/3780350
Additional file 1: Figure S1. of Genome-wide analysis, molecular cloning and expression profiling reveal tissue-specifically expressed, feedback-regulated, stress-responsive and alternatively spliced novel genes involved in gibberellin metabolism in Salvia miltiorrhiza
Creators: name: Du, Qing
name: Caili Li
name: Dongqiao Li
name: Shanfa Lu
Publisher: name: Figshare
Year: 2015
Subjects: subject: Biochemistry
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Evolutionary Biology
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Cancer
subject: 60506 Virology
subject: Computational Biology

description: Conserved domains of enzymes involved in gibberellin metabolism in S. miltiorrhiza. Conserved domains of enzymes involved in gibberellin metabolism in S. miltiorrhiza are shown. (DOC 183 kb)
Prosenoides Brauer & Bergenstamm 1891
Creators: name: Nihei, Silvio S.
Publisher: name: Zenodo
Year: 2016
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Diptera
Tachinidae
Prosenoides

description: Genus Prosenoides Brauer & Bergenstamm
Prosenoides Brauer & Bergenstamm, 1891: 370 (1891: 60). Type species, papilio Brauer & Bergenstamm (mon.) (= curvirostris (Bigot). Refs.: Townsend, 1936a: 136 (in key to Prosenini genera); Townsend, 1938b: 368 (generic diagnosis); Reinhard, 1954: 408 (rev., key); Thompson 1963a: 525 (key to Trinidad genera); Guimarães, 1971a: 32 (cat.); Wood & Zumbado, 2010: 1381 (key to Central American genera of Tachinidae).
Neoprosena Townsend, 1927: 221. Type species, haustellata Townsend (orig. des.).
description: Published as part of Nihei, Silvio S., 2016, FAMILY TACHINIDAE, pp. 904-949 in Zootaxa 4122 (1) on page 909, DOI: 10.11646/zootaxa.4122.1.76, http://zenodo.org/record/257369
Efficient Soft-Chemical Synthesis of Large van-der-Waals Crystals of the Room-Temperature Ferromagnet 1T-CrTe2
Creators: name: Röseler, Kai D.
name: Witteveen, Catherine
name: Besnard, Céline
name: Pomjakushin, Vladimir
name: Jeschke, Harald O.
name: von Rohr, Fabian O.
Publisher: name: arXiv
Year: 2024
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: We herein report on a fast and convenient soft-chemical synthesis approach towards large 1T-CrTe2 van-der-Waals crystals. This compound is formed X-ray diffraction pure, with a complete conversion within just over 2 h from flux-grown LiCrTe2 crystals using diluted acids. Due to the availability of high-quality single crystals, we have confirmed the crystal structure for the first time by single-crystal X-ray diffraction experiments. For the acid deintercalated 1T-CrTe2 crystals, we find long-range ferromagnetic order with a Curie temperature of $T_{\rm C}$ = 318 K. We further revealed the magnetic structure of 1T-CrTe2 using low-temperature neutron powder diffraction experiments and determine the magnetic Hamiltonian using density functional theory. X-ray diffraction experiments of post-annealed crystals suggest a thermal stability of 1T-CrTe2 up to at least 100 °C. Our findings expand the synthesis methods for 1T-CrTe2 crystals, which hold promise for integrated room-temperature spintronics applications.
Additional file 3: Table S2. of Genome-wide analysis, molecular cloning and expression profiling reveal tissue-specifically expressed, feedback-regulated, stress-responsive and alternatively spliced novel genes involved in gibberellin metabolism in Salvia miltiorrhiza
Creators: name: Du, Qing
name: Caili Li
name: Dongqiao Li
name: Shanfa Lu
Publisher: name: Figshare
Year: 2015
Subjects: subject: Biochemistry
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Physiology
subject: Biotechnology
subject: Evolutionary Biology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: Developmental Biology
subject: Cancer
subject: Inorganic Chemistry
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: 60506 Virology
subject: Computational Biology

description: Sequence features of gibberellin metabolism genes in O. sativa. The accession numbers, cDNA length, number of amino acid residues, molecular weight, pI and predicted protein localization are shown. (DOC 73 kb)
Additional file 5: Table S4. of Genome-wide analysis, molecular cloning and expression profiling reveal tissue-specifically expressed, feedback-regulated, stress-responsive and alternatively spliced novel genes involved in gibberellin metabolism in Salvia miltiorrhiza
Creators: name: Du, Qing
name: Caili Li
name: Dongqiao Li
name: Shanfa Lu
Publisher: name: Figshare
Year: 2015
Subjects: subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Genetics
subject: Molecular Biology
subject: Evolutionary Biology
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Marine Biology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: 60506 Virology
subject: Computational Biology

description: Primers used for qRT-PCR. Complete set of primers used for qRT-PCR. (DOC 87 kb)
Helical edge modes in a triangular Heisenberg antiferromagnet
Creators: name: Pradenas, Bastian
name: Adamyan, Grigor
name: Tchernyshyov, Oleg
Publisher: name: arXiv
Year: 2024
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: We investigate the emergence of helical edge modes in a Heisenberg antiferromagnet on a triangular lattice, driven by a topological mechanism similar to that proposed by Dong et al. [Phys. Rev. Lett. 130, 206701 (2023)] for chiral spin waves in ferromagnets. The spin-frame field theory of a three-sublattice antiferromagnet allows for a topological term in the energy that modifies the boundary conditions for certain polarizations of spin waves and gives rise to edge modes. These edge modes are helical: modes with left and right circular polarizations propagate in opposite directions along the boundary in a way reminiscent of the electron edge modes in two-dimensional topological insulators. The field-theoretic arguments are verified in a realistic lattice model of a Heisenberg antiferromagnet with superexchange interactions that exhibits helical edge modes. The strength of the topological term is proportional to the disparity between two inequivalent superexchange paths. These findings suggest potential avenues for realizing magnonic edge states in frustrated antiferromagnets without requiring Dzyaloshinskii-Moriya interactions or nontrivial magnon band topology.
description: 10 pages, 6 figures
Additional file 4: Table S3. of Genome-wide analysis, molecular cloning and expression profiling reveal tissue-specifically expressed, feedback-regulated, stress-responsive and alternatively spliced novel genes involved in gibberellin metabolism in Salvia miltiorrhiza
Creators: name: Du, Qing
name: Caili Li
name: Dongqiao Li
name: Shanfa Lu
Publisher: name: Figshare
Year: 2015
Subjects: subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Evolutionary Biology
subject: Ecology
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Marine Biology
subject: Inorganic Chemistry
subject: FOS: Chemical sciences
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Computational Biology

description: Primers used for full-length coding region cloning. Complete set of primers used for amplication of full-length coding region. (DOC 62 kb)
Prosenoides curvirostris  1889
Creators: name: Nihei, Silvio S.
Publisher: name: Zenodo
Year: 2016
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Diptera
Tachinidae
Prosenoides
Prosenoides curvirostris

description: curvirostris (Bigot), 1889: 264 (Prosena).
Type locality: “ Brazil ”. STs M, F (BMNH). Distr.: Mexico, Central America to Ecuador, Trinidad, Peru and Brazil (Reinhard, 1954: 410; Thompson 1963a: 525). Refs.: Reinhard, 1954: 410 (redesc., key); Thompson 1963a: 525 (redesc., larval desc.); Guimarães, 1971a: 32 (cat.). Comm.: Species not recorded to Colombia, but is likely to occur in the country.
papilio Brauer & Bergenstamm, 1891: 370 (1891: 61).
description: Published as part of Nihei, Silvio S., 2016, FAMILY TACHINIDAE, pp. 904-949 in Zootaxa 4122 (1) on page 909, DOI: 10.11646/zootaxa.4122.1.76, http://zenodo.org/record/257369
Additional file 2: of A hybrid expectation maximisation and MCMC sampling algorithm to implement Bayesian mixture model based genomic prediction and QTL mapping
Creators: name: Tingting Wang
name: Chen, Yi-Ping
name: Bowman, Phil
name: Goddard, Michael
name: Hayes, Ben
Publisher: name: Figshare
Year: 2016
Subjects: subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Ecology
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Plant Biology

description: Calculation of P(i,â  k). (DOCX 21Â kb)
Jeremia Gunther 1930
Creators: name: Lima, Sheila Pereira De
name: Oliveira, Ismael Barreto De
name: Filho, Francisco Felipe Xavier
name: Heleodoro, Raphael Aquino
Publisher: name: Zenodo
Year: 2024
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Phasmida
Phasmatidae
Jeremia

description: Jeremia Günther, 1930
Type. Jeremia grossedentata Redtenbacher, by original monotypy.
Remark. Jeremia may be recognized by both sexes having conspicuous spines at the medioventral carina of mid and posterior legs. Furthermore, females also have spines at meso and metanotum, humps on tergite 7 and by having a prominent gonapophysis 8, which is longer than tergites 8–10 combined (Hennemann & Conle, 2010). As for males, they have a globose head vertex and the subgenital plate (sternite 9) has an indentation at posterior margin (Hennemann & Conle, 2010).
Distribution. Brazil (Roraima [new record]); Bolivia; Ecuador; Peru (Fig. 7A).
description: Published as part of Lima, Sheila Pereira De, Oliveira, Ismael Barreto De, Filho, Francisco Felipe Xavier & Heleodoro, Raphael Aquino, 2024, A new species of Jeremia Redtenbacher (Phasmatodea: Phasmatidae: Cladomorphinae), a stick insect from the northern Brazilian Amazon Basin, pp. 433-445 in Zootaxa 5399 (4) on page 434, DOI: 10.11646/zootaxa.5399.4.8, http://zenodo.org/record/10517192
VIRIS: Simulating indoor airborne transmission combining architectural design and people movement
Creators: name: Xue, Yidan
name: Jabi, Wassim
name: Woolley, Thomas E.
name: Kaouri, Katerina
Publisher: name: arXiv
Year: 2024
Subjects: subject: Computers and Society (cs.CY)
subject: Multiagent Systems (cs.MA)
subject: Physics and Society (physics.soc-ph)
subject: FOS: Computer and information sciences
subject: FOS: Physical sciences

description: A Viral Infection Risk Indoor Simulator (VIRIS) has been developed to quickly assess and compare mitigations for airborne disease spread. This agent-based simulator combines people movement in an indoor space, viral transmission modelling and detailed architectural design, and it is powered by topologicpy, an open-source Python library. VIRIS generates very fast predictions of the viral concentration and the spatiotemporal infection risk for individuals as they move through a given space. The simulator is validated with data from a courtroom superspreader event. A sensitivity study for unknown parameter values is also performed. We compare several non-pharmaceutical interventions (NPIs) issued in UK government guidance, for two indoor settings: a care home and a supermarket. Additionally, we have developed the user-friendly VIRIS web app that allows quick exploration of diverse scenarios of interest and visualisation, allowing policymakers, architects and space managers to easily design or assess infection risk in an indoor space.
Jeremia Gunther 1930
Creators: name: Lima, Sheila Pereira De
name: Oliveira, Ismael Barreto De
name: Filho, Francisco Felipe Xavier
name: Heleodoro, Raphael Aquino
Publisher: name: Zenodo
Year: 2024
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Phasmida
Phasmatidae
Jeremia

description: Key to females of Jeremia (adapted from Hennemann & Conle, 2010)
1 Crest-like projection of tergite 6 nearly indistinct, subgenital plate conspicuously surpassing the apex of abdomen, 2.4 times longer than tergites 8–10 combined....................................................... J. megaplax sp. nov.
1’ Crest-like projection of tergite 6 distinct, subgenital plate slightly surpassing the apex of abdomen, at maximum 1.5 times longer than tergites 8–10 combined....................................................................... 2
2 Body length 136.5–146.0 mm; mesonotum spinose; anteroventral carina of meso- and metafemora smooth; basitarsi lobed dorsally................................................................................ J. grossedentata
2’ Body length 145.0–168.0 mm; mesonotum unarmed; anteroventral carina of meso- and metafemora dentate (Fig. 26); basitarsi simple..................................................................................... J. gymnota
description: Published as part of Lima, Sheila Pereira De, Oliveira, Ismael Barreto De, Filho, Francisco Felipe Xavier & Heleodoro, Raphael Aquino, 2024, A new species of Jeremia Redtenbacher (Phasmatodea: Phasmatidae: Cladomorphinae), a stick insect from the northern Brazilian Amazon Basin, pp. 433-445 in Zootaxa 5399 (4) on page 434, DOI: 10.11646/zootaxa.5399.4.8, http://zenodo.org/record/10517192
Scotiptera Macquart 1835
Creators: name: Nihei, Silvio S.
Publisher: name: Zenodo
Year: 2016
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Diptera
Tachinidae
Scotiptera

description: Genus Scotiptera Macquart
Scotiptera Macquart, 1835: 215. Type species, Dexia melaleuca Wiedemann (subs. des. Macquart, 1844: 240) (= venatoria (Fabricius). Refs.: Curran, 1934a: 492 (key to Guyanan tachinids); Townsend, 1936a: 137 (in key to Prosenini genera); Townsend, 1938b: 376; Guimarães, 1971a: 34 (cat.); Wood & Zumbado, 2010: 1383 (key to Central American genera of Tachinidae).
description: Published as part of Nihei, Silvio S., 2016, FAMILY TACHINIDAE, pp. 904-949 in Zootaxa 4122 (1) on page 909, DOI: 10.11646/zootaxa.4122.1.76, http://zenodo.org/record/257369
Compact Binary Merger Rate with Modified Gravity in Dark-Matter Spikes
Creators: name: Fakhry, Saeed
name: Gholamhoseinian, Sara
name: Farhang, Marzieh
Publisher: name: arXiv
Year: 2024
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: In this study, we investigate the impact of modified gravity on the merger rate of compact binaries within dark-matter spikes surrounding super-massive black holes (SMBHs). Specifically, we calculate binary merger rates involving primordial black holes (PBHs) and/or neutron stars (NSs) in Hu-Sawicki $f(R)$ gravity and the normal branch of Dvali-Gabadadze-Porrati (nDGP) gravity, with three SMBH mass functions, Benson, Vika, and Shankar. The results show consistently higher merger rates predicted for PBH-PBH and PBH-NS binaries in these gravity models compared to general relativity (GR), in particular at lower SMBH masses and for steeper dark-matter spike density profiles. The predicted merger rates are compared to the LIGO-Virgo observations to constrain the parameters of the theory. In particular we find steeper dark-matter spike density profiles in the modified gravity scenarios compared to GR. When compared to current observational constraints on PBH abundance, the mass ranges allowed by Hu-Sawicki $f(R)$ models are found to be wider than by nDGP models, for given merger rates. The results are highly dependent on the choice of SMBH mass function, with Vika and Shankar mass functions predicting lower abundances. The considerable sensitivity of the results on the assumed gravity scenario and SMBH mass function demonstrates the necessity of incorporating the corresponding theoretical uncertainties in making relatively robust predictions on compact binary merger rates and, as a result on PBH properties.
description: 24 pages, 9 figures, refs added, Accepted Version
Jeremia Lima, Oliveira, Filho & Heleodoro, 2024, sp. nov.
Creators: name: Lima, Sheila Pereira De
name: Oliveira, Ismael Barreto De
name: Filho, Francisco Felipe Xavier
name: Heleodoro, Raphael Aquino
Publisher: name: Zenodo
Year: 2024
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Phasmida
Phasmatidae
Jeremia

description: Key to males of Jeremia (from Hennemann & Conle, 2010, excluding J. megaplax sp. nov.)
1 Body length <100 mm; alae reaching half way along abdominal tergite VI; metatibiae with a rounded dorso-apical lobe; basitarsi lobed dorsally.................................................................... J. grossedentata
1’ Body length> 100 mm; alae reaching half way along abdominal tergite V; metatibiae smooth dorsally; basitarsi slender................................................................................................ J. gymnota
description: Published as part of Lima, Sheila Pereira De, Oliveira, Ismael Barreto De, Filho, Francisco Felipe Xavier & Heleodoro, Raphael Aquino, 2024, A new species of Jeremia Redtenbacher (Phasmatodea: Phasmatidae: Cladomorphinae), a stick insect from the northern Brazilian Amazon Basin, pp. 433-445 in Zootaxa 5399 (4) on page 434, DOI: 10.11646/zootaxa.5399.4.8, http://zenodo.org/record/10517192
Far-Infrared and [CII] observations of a z=7 blazar
Creators: name: Banados, Eduardo
name: Khusanova, Yana
name: Decarli, Roberto
name: Momjian, Emmanuel
name: Walter, Fabian
name: Connor, Thomas
name: Carilli, Christopher
name: Mazzucchelli, Chiara
name: Rojas-Ruiz, Sofia
name: Venemans, Bram
Publisher: name: arXiv
Year: 2024
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: We present millimeter observations of the host galaxy of the most distant blazar known, VLASSJ041009.05-013919.88 (hereafter J0410-0139) at z=7, using ALMA and NOEMA observations. The ALMA data reveal a 2e42 erg/s [CII] 158um emission line at z=6.9964 with a [CII]-inferred star-formation rate of 58 Msun/yr. We estimate a dynamical mass of 4.6e9 Msun, implying a black hole mass to host a dynamical mass ratio of 0.15. The 238 GHz continuum (rest-frame IR) decreased by ~33% from the NOEMA to the ALMA observations taken ~10 months apart. The VLA 3-10 GHz radio flux densities showed a ~37% decrease in a similar time frame, suggesting a causal connection. At face value, J0410-0139 would have the lowest [CII]-to-IR luminosity ratio of a z>5.7 quasar reported to date (~1e-4). However, if only <20% of the measured IR luminosity were due to thermal emission from dust, the [CII]-to-IR luminosity ratio would be typical of (U)LIRGS, and the star formation rates derived from [CII] and IR luminosities would be consistent. These results provide further evidence that synchrotron emission significantly contributes to the observed rest-frame IR emission of J0410-0139, similar to what has been reported in some radio-loud AGN at z<1.
description: Version after addressing referee report. See also companion paper: arXiv:2407.07236
Additional file 1: of A hybrid expectation maximisation and MCMC sampling algorithm to implement Bayesian mixture model based genomic prediction and QTL mapping
Creators: name: Tingting Wang
name: Chen, Yi-Ping
name: Bowman, Phil
name: Goddard, Michael
name: Hayes, Ben
Publisher: name: Figshare
Year: 2016
Subjects: subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Molecular Biology
subject: Biotechnology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Ecology
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Plant Biology

description: PEV calculation from GBLUP. (DOCX 16Â kb)
Temporal Elections: Welfare, Strategyproofness, and Proportionality
Creators: name: Elkind, Edith
name: Neoh, Tzeh Yuan
name: Teh, Nicholas
Publisher: name: arXiv
Year: 2024
Subjects: subject: Computer Science and Game Theory (cs.GT)
subject: Artificial Intelligence (cs.AI)
subject: FOS: Computer and information sciences

description: We investigate a model of sequential decision-making where a single alternative is chosen at each round. We focus on two objectives -- utilitarian welfare (Util) and egalitarian welfare (Egal) -- and consider the computational complexity of maximizing these objectives, as well as their compatibility with strategyproofness and proportionality. We observe that maximizing Util is easy, but the corresponding decision problem for Egal is NP-complete even in restricted cases. We complement this hardness result for Egal with parameterized complexity analysis and an approximation algorithm. Additionally, we show that, while a mechanism that outputs an outcome that maximizes Util is strategyproof, all deterministic mechanisms for computing outcomes that maximize Egal fail a very weak variant of strategyproofness, called non-obvious manipulability (NOM). However, we show that when agents have non-empty approval sets at each timestep, choosing an Egal-maximizing outcome while breaking ties lexicographically satisfies NOM. Regarding proportionality, we prove that a proportional (PROP) outcome can be computed efficiently, but finding an outcome that maximizes Util while guaranteeing PROP is NP-hard. We also derive upper and lower bounds on the (strong) price of proportionality with respect to Util and Egal. Some of our results extend to $p$-mean welfare measures other than Egal and Util.
description: Appears in the 27th European Conference on Artificial Intelligence (ECAI), 2024
Generalist Segmentation Algorithm for Photoreceptors Analysis in Adaptive Optics Imaging
Creators: name: Kulyabin, Mikhail
name: Sindel, Aline
name: Pedersen, Hilde
name: Gilson, Stuart
name: Baraas, Rigmor
name: Maier, Andreas
Publisher: name: arXiv
Year: 2024
Subjects: subject: Image and Video Processing (eess.IV)
subject: Computer Vision and Pattern Recognition (cs.CV)
subject: FOS: Electrical engineering, electronic engineering, information engineering
subject: FOS: Computer and information sciences

description: Analyzing the cone photoreceptor pattern in images obtained from the living human retina using quantitative methods can be crucial for the early detection and management of various eye conditions. Confocal adaptive optics scanning light ophthalmoscope (AOSLO) imaging enables visualization of the cones from reflections of waveguiding cone photoreceptors. While there have been significant improvements in automated algorithms for segmenting cones in confocal AOSLO images, the process of labelling data remains labor-intensive and manual. This paper introduces a method based on deep learning (DL) for detecting and segmenting cones in AOSLO images. The models were trained on a semi-automatically labelled dataset of 20 AOSLO batches of images of 18 participants for 0$^{\circ}$, 1$^{\circ}$, and 2$^{\circ}$ from the foveal center. F1 scores were 0.968, 0.958, and 0.954 for 0$^{\circ}$, 1$^{\circ}$, and 2$^{\circ}$, respectively, which is better than previously reported DL approaches. Our method minimizes the need for labelled data by only necessitating a fraction of labelled cones, which is especially beneficial in the field of ophthalmology, where labelled data can often be limited.
Additional file 1: Table S1. of Integrative enrichment analysis: a new computational method to detect dysregulated pathways in heterogeneous samples
Creators: name: Xiangtian Yu
name: Zeng, Tao
name: Guojun Li
Publisher: name: Figshare
Year: 2015
Subjects: subject: Biochemistry
subject: Space Science
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Plant Biology
subject: Computational Biology

description: The 3-order approach-specific datasets corresponding to different methods based on prioritization performance. (DOCX 16 kb)
Additional file 1: Table S1. of Status of hepatic DNA methylome predetermines and modulates the severity of non-alcoholic fatty liver injury in mice
Creators: name: Tryndyak, Volodymyr
name: Han, Tao
name: Fuscoe, James
name: Ross, Sharon
name: Beland, Frederick
name: Pogribny, Igor
Publisher: name: Figshare
Year: 2016
Subjects: subject: Biochemistry
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Biotechnology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences

description: Differentially methylated CpG island (CGI) in promoters of differentially expressed genes in the livers of WSB/EiJ mice fed a CFD diet for 12Â weeks. (DOC 298Â kb)
Scotiptera robusta Curran 1925
Creators: name: Nihei, Silvio S.
Publisher: name: Zenodo
Year: 2016
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Diptera
Tachinidae
Scotiptera
Scotiptera robusta

description: robusta Curran, 1925a: 262. Type locality: Colombia, Magdalena, Sierra San Lorenzo, Hacienda Vista Nieve. HT M (AMNH). Distr.: Colombia. Refs.: Curran, 1925a: 262 (orig. desc.); Guimarães, 1971a: 35 (cat.).
description: Published as part of Nihei, Silvio S., 2016, FAMILY TACHINIDAE, pp. 904-949 in Zootaxa 4122 (1) on page 910, DOI: 10.11646/zootaxa.4122.1.76, http://zenodo.org/record/257369
Renormalization-group running of dimension-8 four-fermion operators in the SMEFT
Creators: name: Boughezal, Radja
name: Huang, Yingsheng
name: Petriello, Frank
Publisher: name: arXiv
Year: 2024
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: We compute the renormalization-group equations governing the evolution of dimension-8 four-fermion operators in the Standard Model Effective Field Theory (SMEFT). We describe the calculation and present analytic results for both the full flavor structure of the SMEFT and with the assumption of minimal flavor violation. We present numerical results for the renormalization-group evolution of the coefficients, and study their impact on fits of the Large Hadron Collider (LHC) Drell-Yan data. The effects of running on the dimension-8 coefficients can reach 50\% or more when evolving from 10 TeV scale down to few-GeV energies relevant for the analysis of fixed-target data. However, the impact of the dimension-8 running on the analysis of Drell-Yan data from the LHC is minimal.
description: 31 pages, 3 tables and 2 figures. Full RGEs without MFV assumption provided in Mathematica attachments; updated to match the published version
Correlation functions of the Kitaev model with a spatially modulated phase in the superconducting order parameter
Creators: name: Cuy, Fabian G. Medina
name: Dolcini, Fabrizio
Publisher: name: arXiv
Year: 2024
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: The Kitaev chain model with a spatially modulated phase in the superconducting order parameter exhibits two types of topological transitions, namely a band topology transition between trivial and topological gapped phases, and a Fermi surface Lifshitz transition from a gapped to a gapless superconducting state. We investigate the correlation functions of the model for arbitrary values of superconducting coupling~$Δ_0$, chemical potential $μ$, and phase modulation wavevector $Q$, characterizing the current flowing through the system. In the cases $μ=0$ or $Q=\pm π/2$ the model turns out to exhibit special symmetries, which are proven to induce an even/odd effect in the correlations as a function of the distance $l$ between two lattice sites, as they are non-vanishing or strictly vanishing depending on the parity of $l$, measured in the lattice spacing unit. We identify a clear difference between the band topology and the Lifshitz transition through the $Q$-dependence of the short distance correlation functions, which, in particular, exhibit pronounced cusps with discontinuous derivatives across the Lifshitz transition. We also determine the long distance behavior of correlations, finding that in the gapped phase there can be various types of exponential decays and that in the gapless phase the algebraic decay is characterized by two different spatial periods, depending on the model parameters. Furthermore, we establish a connection between the gapless superconducting phase of the Kitaev chain and the chiral phase of spin models with Dzyaloshinskii-Moriya interaction.
description: 26 pages, 10 figures
Effective geometry of Bell-network states on a dipole graph
Creators: name: Baytaş, Bekir
name: Yokomizo, Nelson
Publisher: name: arXiv
Year: 2024
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: Bell-network states are a class of entangled states of the geometry that satisfy an area-law for the entanglement entropy in a limit of large spins and are automorphism-invariant, for arbitrary graphs. We present a comprehensive analysis of the effective geometry of Bell-network states on a dipole graph. Our main goal is to provide a detailed characterization of the quantum geometry of a class of diffeomorphism-invariant, area-law states representing homogeneous and isotropic configurations in loop quantum gravity, which may be explored as boundary states for the dynamics of the theory. We found that the average geometry at each node in the dipole graph does not match that of a flat tetrahedron. Instead, the expected values of the geometric observables satisfy relations that are characteristic of spherical tetrahedra. The mean geometry is accompanied by fluctuations with considerable relative dispersion for the dihedral angle, and perfectly correlated for the two nodes.
description: 36 pages, 9 figures
Magnetogenesis from axion-SU(2) inflation
Creators: name: Brandenburg, Axel
name: Iarygina, Oksana
name: Sfakianakis, Evangelos I.
name: Sharma, Ramkishor
Publisher: name: arXiv
Year: 2024
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: We describe a novel proposal for inflationary magnetogenesis by identifying the non-Abelian sector of Spectator Chromo Natural Inflation (SCNI) with the $\rm{SU(2)}_{\rm L}$ sector of the Standard Model. This mechanism relies on the recently discovered attractor of SCNI in the strong backreaction regime, where the gauge fields do not decay on super-horizon scales and their backreaction leads to a stable new trajectory for the rolling axion field. The large super-horizon gauge fields are partly transformed after the electroweak phase transition into electromagnetic fields. The strength and correlation length of the resulting helical magnetic fields depend on the inflationary Hubble scale and the details of the SCNI sector. For suitable parameter choices we show that the strength of the resulting magnetic fields having correlation lengths around $1\, {\rm {Mpc}}$ are consistent with the required intergalactic magnetic fields for explaining the spectra of high energy $γ$ rays from distant blazars.
description: 29 pages, 8 figures, 1 table, Accepted for publication in JCAP
The picasso gas model: Painting intracluster gas on gravity-only simulations
Creators: name: Kéruzoré, F.
name: Bleem, L. E.
name: Frontiere, N.
name: Krishnan, N.
name: Buehlmann, M.
name: Emberson, J. D.
name: Habib, S.
name: Larsen, P.
Publisher: name: arXiv
Year: 2024
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: We introduce picasso, a model designed to predict thermodynamic properties of the intracluster medium based on the properties of halos in gravity-only simulations. The predictions result from the combination of an analytical gas model, mapping gas properties to the gravitational potential, and of a machine learning model to predict the model parameters for individual halos based on their scalar properties, such as mass and concentration. Once trained, the model can be applied to make predictions for arbitrary potential distributions, allowing its use with flexible inputs such as N-body particle distributions or radial profiles. We present the model, and train it using pairs of gravity-only and hydrodynamic simulations. We show that when trained to learn the mapping from gravity-only to non-radiative hydrodynamic simulations, picasso can make remarkably accurate and precise predictions of intracluster gas thermodynamics, with percent-level bias and $\sim 20 \%$ scatter for $r / R_{500c} \in [0.1,1]$. Training the model on hydrodynamic simulations including sub-resolution physics modeling yields robust predictions as well, albeit with the introduction of a radius-dependent bias and an increase in scatter. We further show that the model can be trained to make accurate predictions from very minimal halo information, down to mass and concentration, at the cost of modestly reduced precision. picasso is made publicly available as a Python package at https://github.com/fkeruzore/picasso, which includes trained models that can be used to make predictions easily and efficiently, in a fully auto-differentiable and hardware-accelerated framework
description: Accepted for publication in the Open Journal of Astrophysics; picasso is publicly available at https://github.com/fkeruzore/picasso