cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Leporinus amblyrhynchus Garavello, Britski 1987
Creators: name: Ota, Renata Rúbia
name: Deprá, Gabriel de Carvalho
name: Graça, Weferson Júnio da
name: Pavanelli, Carla Simone
Publisher: name: Zenodo
Year: 2018
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Actinopterygii
Characiformes
Anostomidae
Leporinus
Leporinus amblyrhynchus

description: Leporinus amblyrhynchus Garavello, Britski, 1987 Fig. 4 Body elongated; greatest depth contained 3.8 to 4.3, and caudal peduncle depth 10.0 to 10.2 times in SL; head length 3.9 to 4.0, predorsal distance 2.0, caudal peduncle length 7.0 to 7.9 in SL; snout length 2.0 to 2.5, horizontal orbital diameter 2.9 to 3.8 and least interorbital width 6.7 to 8.4 in HL. Mouth subterminal; premaxilla and dentary with 3 teeth, no maxillary teeth. Lateral line with 37-40 pored scales; transverse series above lateral line with 5 scale rows and below with 4 scale rows. Dorsal fin with 12, pectoral fin with 18, pelvic fin with 9, anal fin with 10 and caudal fin with 19 rays (Garavello, Britski, 1987). Ground color pale yellow; dark-brown longitudinal band along lateral line, from posterior margin of opercle to caudal-fin base; 10-12 dark-brown transverse bars on dorsal surface, extending downward, not reaching longitudal band. Hyaline fins; distal margin of dorsal fin black (Graça, Pavanelli, 2007). Maximum standard length. 100.5 mm (Graça, Pavanelli, 2007). Distribution. Río Paraná basin.
description: Published as part of Ota, Renata Rúbia, Deprá, Gabriel de Carvalho, Graça, Weferson Júnio da & Pavanelli, Carla Simone, 2018, Peixes da planície de inundação do alto rio Paraná e áreas adjacentes: revised, annotated and updated, pp. 1-111 in Neotropical Ichthyology 16 (2) on page 19, DOI: 10.1590/1982-0224-20170094, http://zenodo.org/record/3678395
description: {"references": ["Garavello JC, Britski HA. Duas novas especies do genero Leporinus Spix, 1829, da bacia o alto rio Parana (Teleostei, Anostomidae). Com Mus Cien PUCRS. 1987; 44: 153 - 65.", "Pavanelli CS, Graca WJ, Zawadzki CH, Britski HA, Vidotti AP, Avelino GS, Verissimo S. Fishes from the Corumba Reservoir, Paranaiba River drainage, upper rio Parana basin, State of Goias, Brazil. Check List. 2007; 3 (1): 58 - 64."]}
Rhysodesmus zapotecus
Creators: name: John Hollier
name: Edmund Schiller
name: Nesrine Akkari
Publisher: name: Zenodo
Year: 2017
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Diplopoda
Polydesmida
Xystodesmidae
Rhysodesmus
Rhysodesmus zapotecus

description: zapotecus Saussure, 1860: 314 -315, fig. 11 [Polydesmus].
Régions chaudes du Mexique, San-Andrès-Tuxtla etc. Unspecified number of ♂ and ♀.
 The MHNG collection has one ♀ in the dry collection under the name Fontaria zapotecus, with the data label “Tuztlant [sic], Mexique, M H de Saussure” and there is no reason to doubt that it is a syntype despite Hoffman’s statement (1999: 353) that he could not find any type specimens in the MHNG.
 Rhysodesmus zapotecus (Saussure, 1860)
description: Published as part of John Hollier, Edmund Schiller & Nesrine Akkari, 2017, An annotated list of the Diplopoda described by Aloïs Humbert alone and with Henri de Saussure, and the Diplopoda from Saussure's Mexico expedition, pp. 203-224 in Revue suisse de Zoologie 124 (2) on pages 221-222, DOI: 10.5281/zenodo.893503
title: Politische Partizipation im Medienwandel
Creators: name: Engelmann, Ines
name: Legrand, Marie
name: Marzinkowski, Hanna
Publisher: name: ifpuk - Institute for Media and Communication Studies at FU Berlin
Year: 2019
Subjects: subject: 10504 Political Process, Elections, Political Sociology, Political Culture
subject: 10801 Basic Research, General Concepts and History of the Science of Communication
subject: 1080404 Interactive, electronic Media

description: Politische Partizipation und Medienwandel hängen im Internetzeitalter eng miteinander zusammen. Der Medienwandel kann einerseits Veränderungen in der politischen Beteiligung bedingen, andererseits kann die Ausgestaltung politischer Beteiligung wiederum den Medienwandel vorantreiben. Dabei sind mannigfaltige Ausdrucksformen der politischen Partizipation im und jenseits des Internets denkbar, wobei es von der jeweiligen Wissenschaftsdisziplin abhängt, wo man die Trennlinie zwischen politischer Partizipation oder Nicht-Partizipation zieht.
Dieser Band beschäftigt sich mit aktuellen normativen sowie empirischen Fragen zur politischen Partizipation an der Schnittstelle zwischen Politik- und Kommunikationswissenschaft. Zum einen erweitert der Band unser Wissen über mögliche theoretische, auch interdisziplinäre Perspektiven und Einflussfaktoren, die die politische Beteiligung von „normalen“ Bürgerinnen und Bürgern in ihren zahlreichen Facetten wahrscheinlicher oder unwahrscheinlicher machen. Zum anderen betrachtet ein weiterer Schwerpunkt des Bandes auch die Partizipationsbemühungen politischer Akteure, die Wähler- bzw. Anhängerschaft anzusprechen, zu informieren oder gar zu mobilisieren. Schließlich werden auch die Inhalte politischer Online-Beteiligung erörtert, deren Qualität und deren negative Begleiterscheinungen ebenso, wie mögliche Ursachen und Konsequenzen von mehr oder weniger Qualität.
description: Digital Communication Research
A Wavelet-Based Independence Test for Functional Data With an Application to MEG Functional Connectivity
Creators: name: Miao, Rui
name: Zhang, Xiaoke
name: Wong, Raymond K. W.
Publisher: name: Taylor & Francis
Year: 2022
Subjects: subject: Biochemistry
subject: Biotechnology
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics

description: Measuring and testing the dependency between multiple random functions is often an important task in functional data analysis. In the literature, a model-based method relies on a model which is subject to the risk of model misspecification, while a model-free method only provides a correlation measure which is inadequate to test independence. In this paper, we adopt the Hilbert–Schmidt Independence Criterion (HSIC) to measure the dependency between two random functions. We develop a two-step procedure by first pre-smoothing each function based on its discrete and noisy measurements and then applying the HSIC to recovered functions. To ensure the compatibility between the two steps such that the effect of the pre-smoothing error on the subsequent HSIC is asymptotically negligible when the data are densely measured, we propose a new wavelet thresholding method for pre-smoothing and to use Besov-norm-induced kernels for HSIC. We also provide the corresponding asymptotic analysis. The superior numerical performance of the proposed method over existing ones is demonstrated in a simulation study. Moreover, in a magnetoencephalography (MEG) data application, the functional connectivity patterns identified by the proposed method are more anatomically interpretable than those by existing methods.
Analytical model for collision probability assessments with large satellite constellations
Creators: name: Polli, Eduardo Maria
name: Gonzalo, Juan Luis
name: Colombo, Camilla
Publisher: name: arXiv
Year: 2022
Subjects: subject: Instrumentation and Methods for Astrophysics (astro-ph.IM)
subject: Space Physics (physics.space-ph)
subject: FOS: Physical sciences
subject: 85-10

description: This paper presents an analytical model for collision probability assessments between de-orbiting or injecting space objects and satellite constellations. Considering the first to be subjected to a continuous tangential acceleration, its spiraling motion would result in a series of close approaches in the proximity of a constellation. The proposed methodology involves the integration of the collision probability density function on the encounter plane, from which two analytical formulas, one for the number of close approaches and one for their respective average collision probability, are obtained. The mathematical description of the crossing dynamics relies on the assumption of circular orbits and independent collision probabilities, but does not require to propagate the satellites' orbit. A comparison with a conventional propagation method has been performed for validation purposes, proving its accuracy also in case of elliptical crossing orbits. The model developed has been used to assess the risk connected to constellation's satellites replacement, once they have reached their programmed End-of-Life. The environmental impact of the full replacement of 12 approved constellations is analysed by means of average collision probability. In particular, it is shown that the key features for space exploitation sustainability are the maximum propulsion available from the thruster, the selection of an optimal crossing orbit and the true anomaly phases between constellations' and crossing satellites. The consequences of an in-orbit collision are also investigated by assessing the collision risk generated by the formation of a debris cloud. The results corroborate the need for international standards for space traffic management as an exponentially increasing satellites population could trigger a chain reaction of collisions, making LEO inaccessible for decades.
description: 17 pages, 18 figures, Preprint
Leporinus friderici
Creators: name: Ota, Renata Rúbia
name: Deprá, Gabriel de Carvalho
name: Graça, Weferson Júnio da
name: Pavanelli, Carla Simone
Publisher: name: Zenodo
Year: 2018
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Actinopterygii
Characiformes
Anostomidae
Leporinus
Leporinus friderici

description: Leporinus friderici (Bloch, 1794) Fig. 4 Body elongated; greatest depth contained 3.2 to 4.1, and caudal peduncle depth 9.3 to 10.5 times in SL; head length 4.0 to 4.3, predorsal distance 2.1 to 2.3, caudal peduncle length 8.6 to 10.5 in SL; snout length 2.4 to 2.6, horizontal orbital diameter 3.2 to 3.9 and least interorbital width 2.1 to 2.8. Mouth terminal; premaxilla and dentary with 4 teeth, no maxillary teeth. Lateral line with 37-41 pored scales; transverse series above lateral line with 4-5½ scale rows and below with 4-5½ scale rows. Dorsal fin with 11 or 12, pectoral fin with 15-17, pelvic fin with 9, anal fin with 10 and caudal fin with 19 rays. Ground color silvery to yellowish; superior region of orbit red; three dark-brown rounded or oval, horizontaly elongated, blotches on flank; region of contact between flank scales below lateral line with orange or red spots, forming longitudinal series. Fins yellowish (Graça, Pavanelli, 2007). Maximum standard length. 370.0 mm (Graça, Pavanelli, 2007). Distribution. Drainages of Surinam, Amazon basin and Paraná-Paraguay system.
description: Published as part of Ota, Renata Rúbia, Deprá, Gabriel de Carvalho, Graça, Weferson Júnio da & Pavanelli, Carla Simone, 2018, Peixes da planície de inundação do alto rio Paraná e áreas adjacentes: revised, annotated and updated, pp. 1-111 in Neotropical Ichthyology 16 (2) on page 19, DOI: 10.1590/1982-0224-20170094, http://zenodo.org/record/3678395
description: {"references": ["Pavanelli CS, Graca WJ, Zawadzki CH, Britski HA, Vidotti AP, Avelino GS, Verissimo S. Fishes from the Corumba Reservoir, Paranaiba River drainage, upper rio Parana basin, State of Goias, Brazil. Check List. 2007; 3 (1): 58 - 64."]}
Improving Quantum Computation by Optimized Qubit Routing
Creators: name: Wagner, Friedrich
name: Bärmann, Andreas
name: Liers, Frauke
name: Weissenbäck, Markus
Publisher: name: arXiv
Year: 2022
Subjects: subject: Quantum Physics (quant-ph)
subject: Optimization and Control (math.OC)
subject: FOS: Physical sciences
subject: FOS: Mathematics

description: In this work we propose a high-quality decomposition approach for qubit routing by swap insertion. This optimization problem arises in the context of compiling quantum algorithms onto specific quantum hardware. Our approach decomposes the routing problem into an allocation subproblem and a set of token swapping problems. This allows us to tackle the allocation part and the token swapping part separately. Extracting the allocation part from the qubit routing model of Nannicini et al. (arXiv:2106.06446), we formulate the allocation subproblem as a binary program. Herein, we employ a cost function that is a lower bound on the overall routing problem objective. We strengthen the linear relaxation by novel valid inequalities. For the token swapping part we develop an exact branch-and-bound algorithm. In this context, we improve upon known lower bounds on the token swapping problem. Furthermore, we enhance an existing approximation algorithm. We present numerical results for the integrated allocation and token swapping problem. Obtained solutions may not be globally optimal due to the decomposition and the usage of an approximation algorithm. However, the solutions are obtained fast and are typically close to optimal. In addition, there is a significant reduction in the number of gates and output circuit depth when compared to state-of-the-art heuristics. Reducing these figures is crucial for minimizing noise when running quantum algorithms on near-term hardware. As a consequence, using the novel decomposition approach leads to compiled algorithms with improved quality. Indeed, when compiled with the novel routing procedure and executed on real hardware, our experimental results for quantum approximate optimization algorithms show an significant increase in solution quality in comparison to standard routing methods.
description: Major revision
Fisa descriere si cheie de identificare pentru specia Ondatra zibethicus
Creators: name: Pioarca-Ciocanea, C.M.
name: Manolache, A.S.
name: Rozylowicz, L.
name: Anastasiu, P.
name: Manta, N.
Publisher: name: Zenodo
Year: 2020
Subjects: specii invazive
invasive alien species
Ondatra zibethicus
bizam

description: Fisa descriere si cheie de identificare pentru specia Ondatra zibethicus
description: Managementul adecvat al speciilor invazive din România, în conformitate cu Regulamentul UE 1143/2014 referitor la prevenirea și gestionarea introducerii și răspândirii speciilor alogene invazive, POIM 2014+ 120008, 2018-2022. http://invazive.ccmesi.ro/
Structure, function, and neutralization of SARS-CoV-2 spike glycoproteins
Creators: name: Mannar, Dhiraj
Publisher: name: University of British Columbia
Year: 2023

description: The COVID-19 pandemic erupted in 2019 and went on to have devastating impacts on global health and economies. The causative agent of COVID-19 is a novel coronavirus known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which was found to cause respiratory illness in humans, with symptoms ranging from mild to life threatening (pneumonia, multi-system organ failure). Like previous disease-causing coronaviruses, SARS-CoV-2 relies on a spike glycoprotein to recognize and infect human cells; and antibodies that target the spike protein can prevent viral entry from occurring, effectively neutralizing the virus. However, viruses possess the ability to evolve, and previous experience with other coronaviruses has set the precedence for spike proteins evolving altered antigenic properties and epitopes, permitting escape from neutralizing antibodies. This thesis represents efforts to respond to the COVID-19 pandemic in real time, as we sought to first define the antigenic properties and vulnerabilities of the SARS-CoV-2 spike protein, and then proceed to characterize emerging spike protein mutations and variants, with an emphasis on spike protein structure, receptor binding, and antibody neutralization. We identified antigenic and vulnerable regions in the spike protein amino terminal domain and receptor binding domain and describe heterogenous ways in which antibodies can bind epitopes within these regions. Over the course of the pandemic, significant mutational drift was observed within these regions. We found that mutations within the receptor binding domain were modular in nature, and when combined to represent variant strains of SARS-CoV-2, served to simultaneously prevent recognition of neutralizing antibodies, and enhance or preserve receptor binding affinity. Analysis of variant spike proteins showed that there was high architectural conservation across most variants, with one glaring exception revealing a novel dimers-of-trimers assembly. All variant spike proteins were antibody evasive, with some exhibiting concerning escape from immunized and convalescent sera. Structural analyses on the amino terminal and receptor binding domains of these variants revealed mutational mechanisms underpinning antigenic drift and rationalizing antibody escape. Finally, we structurally defined an epitope on the spike protein that enables broad neutralization of several variants, offering hope for the development of broadly effective therapies to combat variants of SARS-CoV-2.
Three-dimensional contrast transfer function in phase-contrast tomography
Creators: name: Thompson, Darren A.
name: Nesterets, Yakov I.
name: Pavlov, Konstantin M.
name: Gureyev, Timur E.
Publisher: name: arXiv
Year: 2022
Subjects: subject: Medical Physics (physics.med-ph)
subject: Optics (physics.optics)
subject: FOS: Physical sciences

description: A new method is developed for three-dimensional (3D) reconstruction of multi-material objects using propagation-based X-ray phase-contrast tomography (PB-CT) with phase retrieval via the contrast transfer function (CTF) formalism. The approach differs from conventional PB-CT algorithms that apply phase retrieval on individual two-dimensional (2D) projections. Instead, this method involves performing phase retrieval to the CT-reconstructed volume in 3D. The CTF formalism is further extended to the cases of partially-coherent illumination and strongly absorbing samples. Simulated results demonstrate that the proposed post-reconstruction CTF method provides fast and stable phase retrieval, producing results equivalent to conventional pre-reconstruction 2D CTF phase retrieval. Moreover, it is shown that application can be highly localised to isolated objects of interest, without a significant loss of quality, thus leading to increased computational efficiency. Combined with the extended validity of the CTF to greater propagation distances, this method provides additional advantages over approaches based on the transport-of-intensity equation.
description: 11 pages, 5 figures
Leptodesmus zelebori
Creators: name: John Hollier
name: Edmund Schiller
name: Nesrine Akkari
Publisher: name: Zenodo
Year: 2017
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Diplopoda
Polydesmida
Chelodesmidae
Leptodesmus
Leptodesmus zelebori

description: zelebori Humbert & Saussure, 1870: 173 [Polydesmus (Oxyurus)].
Brasilia merid. Unspecified series.
 Saussure & Humbert (1872) gave a more detailed redescription and the locality Rio de Janeiro. No specimens found in the MHNG. There is a broken ♂ syntype with a single gonopod in a vial in the NHMW (Inventory number 3321, Acquisition number 1866.I.6a) (Fig. 2). According to the Acquisition Register the locality is Rio de Janeiro. The generic placement is unclear, and Hoffman, 1979b did not include this species in Leptodesmus.
 Leptodesmus zelebori (Humbert & Saussure, 1870)
description: Published as part of John Hollier, Edmund Schiller & Nesrine Akkari, 2017, An annotated list of the Diplopoda described by Aloïs Humbert alone and with Henri de Saussure, and the Diplopoda from Saussure's Mexico expedition, pp. 203-224 in Revue suisse de Zoologie 124 (2) on page 222, DOI: 10.5281/zenodo.893503
A Wavelet-Based Independence Test for Functional Data with an Application to MEG Functional Connectivity
Creators: name: Miao, Rui
name: Zhang, Xiaoke
name: Wong, Raymond K. W.
Publisher: name: Taylor & Francis
Year: 2021
Subjects: subject: Biochemistry
subject: Biotechnology
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics

description: Measuring and testing the dependency between multiple random functions is often an important task in functional data analysis. In the literature, a model-based method relies on a model which is subject to the risk of model misspecification, while a model-free method only provides a correlation measure which is inadequate to test independence. In this paper, we adopt the Hilbert-Schmidt Independence Criterion (HSIC) to measure the dependency between two random functions. We develop a two-step procedure by first pre-smoothing each function based on its discrete and noisy measurements and then applying the HSIC to recovered functions. To ensure the compatibility between the two steps such that the effect of the pre-smoothing error on the subsequent HSIC is asymptotically negligible when the data are densely measured, we propose a new wavelet thresholding method for pre-smoothing and to use Besov-norm-induced kernels for HSIC. We also provide the corresponding asymptotic analysis. The superior numerical performance of the proposed method over existing ones is demonstrated in a simulation study. Moreover, in an magnetoencephalography (MEG) data application, the functional connectivity patterns identified by the proposed method are more anatomically interpretable than those by existing methods.
Leporinus lacustris Campos 1945
Creators: name: Ota, Renata Rúbia
name: Deprá, Gabriel de Carvalho
name: Graça, Weferson Júnio da
name: Pavanelli, Carla Simone
Publisher: name: Zenodo
Year: 2018
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Actinopterygii
Characiformes
Anostomidae
Leporinus
Leporinus lacustris

description: Leporinus lacustris Campos, 1945 Fig. 4 Body deep; greatest depth contained 2.8 to 3.4 and caudal peduncle depth 6.4 to 8.0 times in SL; head length 3.2 to 3.8, predorsal distance 1.9 to 2.1, caudal peduncle length 13.3 to 13.5 in SL; snout length 1.3 to 2.5, horizontal orbital diameter 3.4 to 4.5 and least interorbital width 1.7 to 2.0. Mouth terminal; premaxilla and dentary with 4 teeth, no maxillary teeth. Lateral line with 32-36 pored scales; transverse series above and below lateral line with 4 or 4½ scale rows. Dorsal fin with 12, pectoral fin with 14-16, pelvic fin with 8 or 9, anal fin with 10 and caudal fin with 19 rays (Campos, 1945; Garavello, 1979). Ground color greyish to pale yellow; three grey to black rounded blotches along lateral line, first and most conspicuous below dorsal fin. Yellowish fins (Graça, Pavanelli, 2007). Maximum standard length. 230.0 mm (Graça, Pavanelli, 2007). Distribution. Paraná-Paraguay system.
description: Published as part of Ota, Renata Rúbia, Deprá, Gabriel de Carvalho, Graça, Weferson Júnio da & Pavanelli, Carla Simone, 2018, Peixes da planície de inundação do alto rio Paraná e áreas adjacentes: revised, annotated and updated, pp. 1-111 in Neotropical Ichthyology 16 (2) on pages 19-20, DOI: 10.1590/1982-0224-20170094, http://zenodo.org/record/3678395
description: {"references": ["Campos AA. Contribuicao ao estudo das especies brasileiras do genero Leporinus. Pap Avulsos Zool. 1945; 5 (16): 141 - 58.", "Garavello JC. Revisao taxonomica do genero Leporinus Spix, 1829 (Ostariophysi, Anostomidae). [PhD Thesis]. Sao Paulo, SP: Universidade de Sao Paulo; 1979.", "Pavanelli CS, Graca WJ, Zawadzki CH, Britski HA, Vidotti AP, Avelino GS, Verissimo S. Fishes from the Corumba Reservoir, Paranaiba River drainage, upper rio Parana basin, State of Goias, Brazil. Check List. 2007; 3 (1): 58 - 64."]}
Native qudit entanglement in a trapped ion quantum processor
Creators: name: Hrmo, Pavel
name: Wilhelm, Benjamin
name: Gerster, Lukas
name: van Mourik, Martin W.
name: Huber, Marcus
name: Blatt, Rainer
name: Schindler, Philipp
name: Monz, Thomas
name: Ringbauer, Martin
Publisher: name: arXiv
Year: 2022
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: Quantum information carriers, just like most physical systems, naturally occupy high-dimensional Hilbert spaces. Instead of restricting them to a two-level subspace, these high-dimensional (qudit) quantum systems are emerging as a powerful resource for the next generation of quantum processors. Yet harnessing the potential of these systems requires efficient ways of generating the desired interaction between them. Here, we experimentally demonstrate an implementation of a native two-qudit entangling gate in a trapped-ion qudit system up to dimension $5$. This is achieved by generalizing a recently proposed light-shift gate mechanism to generate genuine qudit entanglement in a single application of the gate. The gate seamlessly adapts to the local dimension of the system with a calibration overhead that is independent of the dimension.
description: 9 pages, 5 figures
The role of mucus-derived monosaccharides in the fitness of the enteric pathogen Citrobacter rodentium
Creators: name: Mslati, Matthias Ahmad
Publisher: name: University of British Columbia
Year: 2023

description: Background The nutritional program(s) used by enteric bacterial pathogens to colonize their host’s intestines remain unclear. To begin to understand this question, we focused on the enteric murine pathogen Citrobacter rodentium. C. rodentium has to cross a thick mucus barrier, which is primarily made up of Muc2 glycoprotein, during its infection of the large intestine. As a glycoprotein, Muc2-linked sugars can constitute a potential nutrient source for C. rodentium. This thesis examined the nutritional role and dynamic changes of Muc2-linked sugars during C. rodentium infection. Methods In vitro growth assays were used to assess whether C. rodentium can utilize the Muc2-linked sugars: N-acetylglucosamine (GlcNAc), N-acetylgalactosamine (GalNAc), N-acetylneuraminic acid (NeuNAc), galactose (Gal), and fucose (Fuc). Stool samples of mice at baseline and during different stages of C. rodentium infection were analyzed for the sugar concentration using an advanced quantitative technique termed UHPLC/QqQ-MS. Lastly, mutant strains of C. rodentium lacking key genes for the metabolism of Muc2-linked sugars were generated and assessed for their fitness to colonize and cause pathological damage to mice. Results We found that C. rodentium was able to grow on the Muc2-linked sugars: GlcNAc, NeuNAc, and Gal. We quantified the levels of these 3 sugars in the stool samples of mice, and determined that they are primarily Muc2 derived and that GlcNAc levels are increased during C. rodentium infection. In vivo competition experiments revealed that C. rodentium mutant strains with defects in two or more of the Muc2-linked sugar pathways were outcompeted by the wild type (WT) strain. Lastly, a C. rodentium mutant strain unable to use all 3 sugars (Δ3) displayed a significant delay in colonizing mice and reaching the intestinal epithelium. As a result, the majority of mice infected with this mutant displayed no pathological damage to their colons, indicating a major defect in virulence. Conclusions We show that the intestinal Muc2-linked sugars serve as critical nutrient sources for C. rodentium during colonization of the mouse intestine, and that the levels of Muc2-linked sugars are influenced by C. rodentium infection suggesting a potential role of C. rodentium in shaping the nutrient environment in the intestine.
Practitioners preference in using electrotherapy to treat paediatric lower limb conditions: an online survey
Creators: name: Ho, Malia
name: Pacey, Verity
name: Paterson, Kade
name: Griffiths, Ian
name: Tofts, Louise
name: Davies, Luke
name: Williams, Cylie
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Medicine
subject: Cell Biology
subject: Pharmacology
subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: Environmental Sciences not elsewhere classified
subject: Sociology
subject: FOS: Sociology
subject: Biological Sciences not elsewhere classified
subject: Science Policy

description: Electrotherapies are commonly used to treat adult musculoskeletal pathologies. However, there is insufficient evidence supporting the use of electrotherapies for lower limb conditions in children. Currently, it is unknown how electrotherapies are used in paediatric clinical practice. This study aimed to investigate if practitioners use electrotherapy to treat children’s lower limb conditions, frequency and why. A custom-built online survey was disseminated via social media targeting international medical and healthcare practitioners who treat children with lower limb conditions using electrotherapy. Practitioners were asked if they did or did not use electrotherapies, and their reasons. Responses were described in frequencies and with thematic analysis. There were 445 practitioners who responded. From these, 301(68%) indicated they used electrotherapy, with the most frequently used being Transcutaneous Electrical Nerve Stimulation (n = 110). The most common reason cited for using electrotherapy was practitioner preference due to the alleged effectiveness of the chosen modality. The remaining 144 (32%) practitioners reported not using electrotherapy, the most common reason being lack of evidence. We found that a majority of practitioners used electrotherapies on children. The reasons for using or not using electrotherapy were practitioner centred. Electrotherapy modalities are commonly used to treat musculoskeletal injuries in adultsThe management of children differs from adults due to physiological and psychological differences.The use of electrotherapy to treat musculoskeletal lower limb pathologies children is currently not supported by evidence, and the frequency of use of these modalities in children is not known.This study found that despite that, a majority of medical and health practitioners surveyed in this study routinely use electrotherapy to treat paediatric musculoskeletal injuries. Electrotherapy modalities are commonly used to treat musculoskeletal injuries in adults The management of children differs from adults due to physiological and psychological differences. The use of electrotherapy to treat musculoskeletal lower limb pathologies children is currently not supported by evidence, and the frequency of use of these modalities in children is not known. This study found that despite that, a majority of medical and health practitioners surveyed in this study routinely use electrotherapy to treat paediatric musculoskeletal injuries.
DSCA: A Dual-Stream Network with Cross-Attention on Whole-Slide Image Pyramids for Cancer Prognosis
Creators: name: Liu, Pei
name: Fu, Bo
name: Ye, Feng
name: Yang, Rui
name: Xu, Bin
name: Ji, Luping
Publisher: name: arXiv
Year: 2022
Subjects: subject: Image and Video Processing (eess.IV)
subject: Computer Vision and Pattern Recognition (cs.CV)
subject: Machine Learning (cs.LG)
subject: FOS: Electrical engineering, electronic engineering, information engineering
subject: FOS: Computer and information sciences

description: The cancer prognosis on gigapixel Whole-Slide Images (WSIs) has always been a challenging task. To further enhance WSI visual representations, existing methods have explored image pyramids, instead of single-resolution images, in WSIs. In spite of this, they still face two major problems: high computational cost and the unnoticed semantical gap in multi-resolution feature fusion. To tackle these problems, this paper proposes to efficiently exploit WSI pyramids from a new perspective, the dual-stream network with cross-attention (DSCA). Our key idea is to utilize two sub-streams to process the WSI patches with two resolutions, where a square pooling is devised in a high-resolution stream to significantly reduce computational costs, and a cross-attention-based method is proposed to properly handle the fusion of dual-stream features. We validate our DSCA on three publicly-available datasets with a total number of 3,101 WSIs from 1,911 patients. Our experiments and ablation studies verify that (i) the proposed DSCA could outperform existing state-of-the-art methods in cancer prognosis, by an average C-Index improvement of around 4.6%; (ii) our DSCA network is more efficient in computation -- it has more learnable parameters (6.31M vs. 860.18K) but less computational costs (2.51G vs. 4.94G), compared to a typical existing multi-resolution network. (iii) the key components of DSCA, dual-stream and cross-attention, indeed contribute to our model's performance, gaining an average C-Index rise of around 2.0% while maintaining a relatively-small computational load. Our DSCA could serve as an alternative and effective tool for WSI-based cancer prognosis.
description: 12 pages, 6 figures, 7 tables
Infrared acceleration radiation
Creators: name: Good, Michael R. R.
name: Davies, Paul C. W.
Publisher: name: arXiv
Year: 2022
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: High Energy Physics - Theory (hep-th)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We present an exactly soluble electron trajectory that permits an analysis of the soft (deep infrared) radiation emitted, the existence of which has been experimentally observed during beta decay via lowest order inner bremsstrahlung. Our treatment also predicts the time evolution and temperature of the emission, and possibly the spectrum, by analogy with the closely related phenomenon of the dynamic Casimir effect.
description: 4 pages, 5 figures
Leporinus octofasciatus Steindachner 1915
Creators: name: Ota, Renata Rúbia
name: Deprá, Gabriel de Carvalho
name: Graça, Weferson Júnio da
name: Pavanelli, Carla Simone
Publisher: name: Zenodo
Year: 2018
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Actinopterygii
Characiformes
Anostomidae
Leporinus
Leporinus octofasciatus

description: Leporinus octofasciatus Steindachner, 1915 Fig. 4 Body elongated; greatest depth contained 3.6 to 3.8, and caudal peduncle depth 9.1 to 9.3 times in SL; head length 3.1 to 4.3, predorsal distance 1.9 to 2.1, caudal peduncle length 9.2 to 9.3 in SL; snout length 2.2 to 2.7, horizontal orbital diameter 4.0 to 4.2 and least interorbital width 2.2 to 2.6. Mouth terminal; premaxilla with 3 and dentary with 4 teeth, no maxillary teeth. Lateral line with 35-39 pored scales; transverse series above lateral line with 5 scale rows and below with 4-5 scale rows. Dorsal fin with 12, pectoral fin with 16 or 17, pelvic fin with 9, anal fin with 9 or 10 and caudal fin with 19 rays (Britski, Garavello, 1978; Garavello, 1979). Ground color pale yellow; eight black transverse bars on body (posterior to head). Reddish fins (Graça, Pavanelli, 2007). Maximum standard length. 210.0 mm (Graça, Pavanelli, 2007). Distribution. Rio Cubatão (State of Santa Catarina) and río Paraná basin.
description: Published as part of Ota, Renata Rúbia, Deprá, Gabriel de Carvalho, Graça, Weferson Júnio da & Pavanelli, Carla Simone, 2018, Peixes da planície de inundação do alto rio Paraná e áreas adjacentes: revised, annotated and updated, pp. 1-111 in Neotropical Ichthyology 16 (2) on page 20, DOI: 10.1590/1982-0224-20170094, http://zenodo.org/record/3678395
description: {"references": ["Britski HA, Garavello JC. Sobre Leporinus octofasciatus Steindachner da bacia do rio Parana (Pisces, Anostomidae). Pap Avulsos Zool. 1978; 31 (16): 237 - 50.", "Garavello JC. Revisao taxonomica do genero Leporinus Spix, 1829 (Ostariophysi, Anostomidae). [PhD Thesis]. Sao Paulo, SP: Universidade de Sao Paulo; 1979.", "Pavanelli CS, Graca WJ, Zawadzki CH, Britski HA, Vidotti AP, Avelino GS, Verissimo S. Fishes from the Corumba Reservoir, Paranaiba River drainage, upper rio Parana basin, State of Goias, Brazil. Check List. 2007; 3 (1): 58 - 64."]}
Marginal quenches and drives in Tomonaga-Luttinger liquids
Creators: name: Datta, Shouvik
name: Lapierre, Bastien
name: Moosavi, Per
name: Tiwari, Apoorv
Publisher: name: arXiv
Year: 2022
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: Quantum Gases (cond-mat.quant-gas)
subject: High Energy Physics - Theory (hep-th)
subject: Mathematical Physics (math-ph)
subject: FOS: Physical sciences

description: We study Tomonaga-Luttinger liquids thrown out of equilibrium by marginal deformations in the form of interaction modulations. This is modeled by quenching or periodically driving the Luttinger parameter or, equivalently, the compactification radius of the free boson conformal field theory between two different values. We obtain exact analytical results for the evolution of the Loschmidt echo and observables such as the particle and energy densities. Starting from generic initial states, the quench dynamics are shown to exhibit revivals and temporal orthogonalities. For the periodic drive, we show stability or instability of time-evolved physical quantities dependent on the drive parameters. We also compare the corresponding marginally deformed thermal density matrices by non-perturbatively evaluating their Rényi divergence as a Euclidean quench. All the dynamics are shown to be crucially dependent on the ratio of the Luttinger parameters, which corresponds to the Zamolodchikov distance in the space of marginal deformations. Our setup is equivalently interpreted as the dynamics of the bosonic string upon instantaneous changes of the target-space radius.
description: 64 pages, LaTeX, 12 figures; minor updates and typos corrected; final published version
Rhysodesmus zendalus
Creators: name: John Hollier
name: Edmund Schiller
name: Nesrine Akkari
Publisher: name: Zenodo
Year: 2017
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Diplopoda
Polydesmida
Xystodesmidae
Rhysodesmus
Rhysodesmus zendalus

description: zendalus Humbert & Saussure, 1869a: 150 [Polydesmus (Fontaria)].
Mexico orientalis. Unspecified number of ♂ and ♀.
 Saussure & Humbert (1872) gave a more detailed redescription, and the locality “Cordillère orientale.” The MHNG collection has one ♂ and one ♀ in alcohol under the name Fontaria zendala, and labelled as types. The data label in the jar reads “Moyoapan, Mexique”. The ♂ was designated as lectotype by Hoffman (1970: 157).
 Rhysodesmus zendalus (Humbert & Saussure, 1869)
description: Published as part of John Hollier, Edmund Schiller & Nesrine Akkari, 2017, An annotated list of the Diplopoda described by Aloïs Humbert alone and with Henri de Saussure, and the Diplopoda from Saussure's Mexico expedition, pp. 203-224 in Revue suisse de Zoologie 124 (2) on page 222, DOI: 10.5281/zenodo.893503
Leporinus striatus Kner 1858
Creators: name: Ota, Renata Rúbia
name: Deprá, Gabriel de Carvalho
name: Graça, Weferson Júnio da
name: Pavanelli, Carla Simone
Publisher: name: Zenodo
Year: 2018
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Actinopterygii
Characiformes
Anostomidae
Leporinus
Leporinus striatus

description: Leporinus striatus Kner, 1858 Fig. 4 Body elongated; greatest depth contained 3.9 to 4.0, and caudal peduncle depth 9.6 to 10.6 times in SL; head length 3.7 tp 4.5, predorsal distance 2.1 to 2.2, caudal peduncle length 9.4 to 10.4 in SL; snout length 2.2 to 2.8, horizontal orbital diameter 3.1 to 3.5 and least interorbital width 2.5 to 2.7 in HL. Mouth terminal; premaxilla with 3, dentary with 4 teeth, no maxillary teeth. Lateral line with 34-36 pored scales; transverse series above lateral line with 4 or 4½ scale rows and below with 4 scale rows. Dorsal fin with 12, pectoral fin with 16 or 17, pelvic fin with 9 or 10 rays, anal fin with 10 and caudal fin with 19 rays (Garavello, 1979). Ground color pale yellow; four dark-brown longitudinal bands on body, the superior one sometimes fused. Yellowish fins (Graça, Pavanelli, 2007). Maximum standard length. 83.2 mm (Graça, Pavanelli, 2007). Distribution. Paraná-Paraguay system.
description: Published as part of Ota, Renata Rúbia, Deprá, Gabriel de Carvalho, Graça, Weferson Júnio da & Pavanelli, Carla Simone, 2018, Peixes da planície de inundação do alto rio Paraná e áreas adjacentes: revised, annotated and updated, pp. 1-111 in Neotropical Ichthyology 16 (2) on page 20, DOI: 10.1590/1982-0224-20170094, http://zenodo.org/record/3678395
description: {"references": ["Garavello JC. Revisao taxonomica do genero Leporinus Spix, 1829 (Ostariophysi, Anostomidae). [PhD Thesis]. Sao Paulo, SP: Universidade de Sao Paulo; 1979.", "Pavanelli CS, Graca WJ, Zawadzki CH, Britski HA, Vidotti AP, Avelino GS, Verissimo S. Fishes from the Corumba Reservoir, Paranaiba River drainage, upper rio Parana basin, State of Goias, Brazil. Check List. 2007; 3 (1): 58 - 64."]}
An Interior-Point-Inspired algorithm for Linear Programs arising in Discrete Optimal Transport
Creators: name: Zanetti, Filippo
name: Gondzio, Jacek
Publisher: name: arXiv
Year: 2022
Subjects: subject: Optimization and Control (math.OC)
subject: FOS: Mathematics

description: Discrete Optimal Transport problems give rise to very large linear programs (LP) with a particular structure of the constraint matrix. In this paper we present a hybrid algorithm that mixes an interior point method (IPM) and column generation, specialized for the LP originating from the Kantorovich Optimal Transport problem. Knowing that optimal solutions of such problems display a high degree of sparsity, we propose a column-generation-like technique to force all intermediate iterates to be as sparse as possible. The algorithm is implemented nearly matrix-free. Indeed, most of the computations avoid forming the huge matrices involved and solve the Newton system using only a much smaller Schur complement of the normal equations. We prove theoretical results about the sparsity pattern of the optimal solution, exploiting the graph structure of the underlying problem. We use these results to mix iterative and direct linear solvers efficiently, in a way that avoids producing preconditioners or factorizations with excessive fill-in and at the same time guaranteeing a low number of conjugate gradient iterations. We compare the proposed method with two state-of-the-art solvers and show that it can compete with the best network optimization tools in terms of computational time and memory usage. We perform experiments with problems reaching more than four billion variables and demonstrate the robustness of the proposed method.
MOESM14 of Mitochondrial genome in Hypsizygus marmoreus and its evolution in Dikarya
Creators: name: Wang, Gang
name: Lin, Jingxian
name: Shi, Yang
name: Chang, Xiaoguang
name: Wang, Yuanyuan
name: Guo, Lin
name: Wang, Wenhui
name: Dou, Meijie
name: Deng, Youjin
name: Ming, Ray
name: Zhang, Jisen
Publisher: name: figshare
Year: 2019
Subjects: subject: Biochemistry
subject: Genetics
subject: FOS: Biological sciences
subject: Evolutionary Biology
subject: Sociology
subject: FOS: Sociology
subject: Biological Sciences not elsewhere classified
subject: Infectious Diseases
subject: FOS: Health sciences

description: Additional file 14: Table S8. The distances between nad2, nad3 and between nad4L, nad5.
Learning block structured graphs in Gaussian graphical models
Creators: name: Colombi, Alessandro
name: Argiento, Raffaele
name: Paci, Lucia
name: Pini, Alessia
Publisher: name: arXiv
Year: 2022
Subjects: subject: Methodology (stat.ME)
subject: FOS: Computer and information sciences

description: Within the framework of Gaussian graphical models, a prior distribution for the underlying graph is introduced to induce a block structure in the adjacency matrix of the graph and learning relationships between fixed groups of variables. A novel sampling strategy named Double Reversible Jumps Markov chain Monte Carlo is developed for block structural learning, under the conjugate G-Wishart prior. The algorithm proposes moves that add or remove not just a single link but an entire group of edges. The method is then applied to smooth functional data. The classical smoothing procedure is improved by placing a graphical model on the basis expansion coefficients, providing an estimate of their conditional independence structure. Since the elements of a B-Spline basis have compact support, the independence structure is reflected on well-defined portions of the domain. A known partition of the functional domain is exploited to investigate relationships among the substances within the compound.
Topological types of actions on curves
Creators: name: Conti, Diego
name: Ghigi, Alessandro
name: Pignatelli, Roberto
Publisher: name: arXiv
Year: 2022
Subjects: subject: Algebraic Geometry (math.AG)
subject: FOS: Mathematics
subject: 14H37 (Primary) 14Q05, 57M60, 14H15, 14J10 (Secondary)

description: We describe an algorithm that constructs a list of all topological types of holomorphic actions of a finite group on a compact Riemann surface $C$ of genus at least $g \geq 2$ with $C/G \cong \mathbb{P}^1$.
description: v2: corrected definition of Hurwitz equivalence using the braid group
Seismic behaviour of concrete wall bridge pier reinforced with Shape Memory Alloy
Creators: name: Ahmad, Nursafarina
Publisher: name: University of British Columbia
Year: 2023

description: Reinforced concrete bridge (RC) was designed with high ductility and built-in high seismic areas to prevent collapse from a seismic event. During Hashin-Hawaii seismic event in 1995, it was observed that bridge wall pier performance in a weak direction is still far from the acceptable level. The bridge wall pier suffered from high residual drift making the bridge unserviceable. The performance-based seismic design (PBSD) is a comprehensive method that limits the local and global deformation of the bridge to the acceptable design load level. The objective of PBSD can be accomplished by implementing Shape Memory Alloy (SMA) as a reinforcement bar to enhance seismic performance in concrete bridge piers. This research aims to investigate the seismic behavior in weak directions for wall bridge pier reinforced with shape memory alloy. To provide comprehensive information, this study started with a parametric study to evaluate the influence of geometry and material properties using fractional factorial analysis. The test results were explored to evaluate the influence of concrete strength, steel yield strength, SMA yield strength, longitudinal and transverse reinforcement ratio, aspect ratio, and skew angle. In addition, the aspect ratio result was calibrated with experimental work. The seismic performance of a 1/3 scaled wall pier reinforced with SMA was investigated experimentally using lateral cyclic loading in the weak direction. In addition, the test result was compared to the conventional reinforced concrete wall in terms of hysteretic curves, maximum and residual drift, displacement recovery capacity, and energy dissipation. The quantitative damage states associated with different performance levels (cracking, yielding, spalling, and crushing) for RC wall pier reinforced with three different types of SMAs were developed using Incremental Dynamic Analysis (IDA). Based on an extensive numerical study using IDA, the effect of compressive strength, aspect ratio, and longitudinal and transverse reinforcement ratio was evaluated for three different types of SMAs. Finally, vulnerability curves are established for three different RC-SMA wall piers using maximum and residual drift as engineering demand parameters. It was discovered that the RC- SMA wall pier has a low probability of damage and minimizes residual drift, which significantly contributes to the life cycle cost benefit.
Comparing cubical and globular directed paths
Creators: name: Gaucher, Philippe
Publisher: name: arXiv
Year: 2022
Subjects: subject: Category Theory (math.CT)
subject: Algebraic Topology (math.AT)
subject: FOS: Mathematics

description: A flow is a directed space structure on a homotopy type. It is already known that the underlying homotopy type of the realization of a precubical set as a flow is homotopy equivalent to the realization of the precubical set as a topological space. This realization depends on the non-canonical choice of a q-cofibrant replacement. We construct a new realization functor from precubical sets to flows which is homotopy equivalent to the previous one and which does not depend on the choice of any cofibrant replacement functor. The main tool is the notion of natural $d$-path introduced by Raussen. The flow we obtain for a given precubical set is not anymore q-cofibrant but is still m-cofibrant. As an application, we prove that the space of execution paths of the realization of a precubical set as a flow is homotopy equivalent to the space of nonconstant $d$-paths between vertices in the geometric realization of the precubical set.
description: 24 pages; last section rewritten due to a mistake in the proof of the main theorem: notion of spatial precubical set introduced