cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Lentilactobacillus raoultii Zheng, Wittouck, Salvetti, Franz, Harris, Mattarelli, O'Toole, Pot, Vandamme, Walter, Watanabe, Wuyts, Felis, Gänzle & Lebeer, 2020, SP. NOV.
Creators: name: Zheng, Jinshui
name: Wittouck, Stijn
name: Salvetti, Elisa
name: Franz, Charles M. A. P.
name: Harris, Hugh M. B.
name: Mattarelli, Paola
name: O'Toole, Paul W.
name: Pot, Bruno
name: Vandamme, Peter
name: Walter, Jens
name: Watanabe, Koichi
name: Wuyts, Sander
name: Felis, Giovanna E.
name: Gänzle, Michael G.
name: Lebeer, Sarah
Publisher: name: Zenodo
Year: 2020
Subjects: Biodiversity
Taxonomy
Bacteria
Firmicutes
Bacilli
Lactobacillales
Lactobacillaceae
Lentilactobacillus
Lentilactobacillus raoultii

description: DESCRIPTIONOF LENTILACTOBACILLUS RAOULTII SP. NOV.
Lentilactobacillus raoultii (ra.oul’ti.i. N.L. gen. n. raoultii of Raoult, named after the microbiologist Didier Raoult).
Thespecies was effectively but not validlypublished as Lactobacillus raoultii Nicaise et al. 2019 [337]. Growth is observed between 25–45°C and between pH 5 and 7.5; the genome size of the type strain is 3.07 Mbp. The mol% G+C content of DNAis 41.4.
Isolated from the vagina of a healthy women.
Thetypestrainis Strain Marseille P4006 T = CSUR P4006 T =LMG 31598 T = CCUG 71848 T.
Genome sequence accession number: OVSN00000000.
16S rRNA gene accession number: LT854294.
description: Published as part of Zheng, Jinshui, Wittouck, Stijn, Salvetti, Elisa, Franz, Charles M. A. P., Harris, Hugh M. B., Mattarelli, Paola, O'Toole, Paul W., Pot, Bruno, Vandamme, Peter, Walter, Jens, Watanabe, Koichi, Wuyts, Sander, Felis, Giovanna E., Gänzle, Michael G. & Lebeer, Sarah, 2020, A taxonomic note on the genus Lactobacillus: Description of 23 novel genera, emended description of the genus Lactobacillus Beijerinck 1901, and union of Lactobacillaceae and Leuconostocaceae, pp. 2782-2858 in International Journal of Systematic and Evolutionary Microbiology 70 on page 2846, DOI: 10.1099/ijsem.0.004107, http://zenodo.org/record/4730536
Intermittent Giant Goos-Hanchen shifts from Airy beams at nonlinear interfaces
Creators: name: Chamorro-Posada, Pedro
name: Sánchez-Curto, Julio
name: Aceves, Alejandro B.
name: McDonald, Graham S.
Publisher: name: arXiv
Year: 2013
Subjects: subject: Optics (physics.optics)
subject: Pattern Formation and Solitons (nlin.PS)
subject: FOS: Physical sciences

description: We study the giant Goos-Hanchen shift obtained from an Airy beam impinging on a nonlinear interface. To avoid any angular restriction associated with the paraxial approximation, the analysis is based on the numerical solution of the nonlinear Helmholtz equation. We report the existence of non-standard intermittent and oscillatory regimes for the nonlinear Goos-Hanchen shifts which can be explained in terms of the competition between the critical coupling to a surface mode of the reflected component of the Airy beam and the soliton emission from the refracted beam component.
description: Some typos corrected and other minor changes
Topological Boundary Modes in Isostatic Lattices
Creators: name: Kane, C. L.
name: Lubensky, T. C.
Publisher: name: arXiv
Year: 2013
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Soft Condensed Matter (cond-mat.soft)
subject: FOS: Physical sciences

description: Frames, or lattices consisting of mass points connected by rigid bonds or central force springs, are important model constructs that have applications in such diverse fields as structural engineering, architecture, and materials science. The difference between the number of bonds and the number of degrees of freedom of these lattices determines the number of their zero-frequency "floppy modes". When these are balanced, the system is on the verge of mechanical instability and is termed isostatic. It has recently been shown that certain extended isostatic lattices exhibit floppy modes localized at their boundary. These boundary modes are insensitive to local perturbations, and appear to have a topological origin, reminiscent of the protected electronic boundary modes that occur in the quantum Hall effect and in topological insulators. In this paper we establish the connection between the topological mechanical modes and the topological band theory of electronic systems, and we predict the existence of new topological bulk mechanical phases with distinct boundary modes. We introduce model systems in one and two dimensions that exemplify this phenomenon.
description: 8 pages, 5 figures, including supplementary information
Bioconductor packages for analysis of Thermal Proteome Profiling data
Creators: name: Kurzawa, Nils
name: Childs, Dorothee
name: Franken, Holger
name: Savitski, Mikhail M.
name: Huber, Wolfgang
Publisher: name: F1000 Research Limited
Year: 2020

description: Thermal proteome profiling (TPP) is a mass spectrometry-based technology which was originally developed to identify drug (off-)targets on a proteome-wide scale. The assay is built on the principle of the cellular thermal shift assay which is that proteins inside living cells may be modulated in their thermal stability by ligand binding. This can be read out by shifts of melting profiles of respective proteins. Soon after TPP was established, a first Bioconductor package TPP was released, which implemented a method to infer ligand-protein interactions using shifts of melting points. The realization that this procedure lacks sensitivity to detect proteins with e.g. very high thermal stability lead to the development of the NPARC package. Further, it was realized that TPP data can also inform on protein-protein interaction (PPI) dynamics. Another Bioconductor package Rtpca was thus implemented to accomodate respective analyses. Lastly, the experimental setup of TPP experiments was expanded to profile ligand dose and temperature ranges together to improve sensitivity. To accomodate the different data structure and different required statistical analysis the package TPP2D was created. Here, the different functionalities of these packages are presented.
Additional file 1 of A comparative proteomic analysis provides insight into the molecular mechanism of bud break in longan
Creators: name: Jue, Dengwei
name: Liu, Liqin
name: Sang, Xuelian
name: Shi, Shengyou
Publisher: name: figshare
Year: 2022
Subjects: subject: Biochemistry
subject: Cell Biology
subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: Ecology
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Inorganic Chemistry
subject: FOS: Chemical sciences
subject: Plant Biology

description: Supplementary Material 1
Kelvin-Helmholtz Instability in non-Newtonian Complex Plasma
Creators: name: Banerjee, D.
name: Garai, S.
name: Janaki, M. S.
name: Chakrabarti, N.
Publisher: name: arXiv
Year: 2013
Subjects: subject: Plasma Physics (physics.plasm-ph)
subject: FOS: Physical sciences

description: The Kelvin-Helmholtz (KH) instability is studied in a non-Newtonian dusty plasma with an experimentally verified model [Phys. Rev. Lett. {\bf 98}, 145003 (2007)] of shear flow rate dependent viscosity. The shear flow profile used here is a parabolic type bounded flow. Both the shear thinning and shear thickening properties are investigated in compressible as well as incompressible limits using a linear stability analysis. Like the stabilizing effect of compressibility on the KH instability, the non-Newtonian effect in shear thickening regime could also suppress the instability but on the contrary, shear thinning property enhances it. A detailed study is reported on the role of non-Newtonian effect on KH instability with conventional dust fluid equations using standard eigenvalue analysis.
description: 13 pages, 4 figures
Curvilinear Grids for WENO Methods in Astrophysical Simulations
Creators: name: Grimm-Strele, Hannes
name: Kupka, Friedrich
name: Muthsam, Herbert J.
Publisher: name: arXiv
Year: 2013
Subjects: subject: Computational Physics (physics.comp-ph)
subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: Numerical Analysis (math.NA)
subject: FOS: Physical sciences
subject: FOS: Mathematics

description: We investigate the applicability of curvilinear grids in the context of astrophysical simulations and WENO schemes. With the non-smooth mapping functions from Calhoun et al. (2008), we can tackle many astrophysical problems which were out of scope with the standard grids in numerical astrophysics. We describe the difficulties occurring when implementing curvilinear coordinates into our WENO code, and how we overcome them. We illustrate the theoretical results with numerical data. The WENO finite difference scheme works only for high Mach number flows and smooth mapping functions whereas the finite volume scheme gives accurate results even for low Mach number flows and on non-smooth grids.
description: 27 pages, 10 figures, accepted for publication in CPC
Lentilactobacillus rapi Zheng & Wittouck & Salvetti & Franz & Harris & Mattarelli & O'Toole & Pot & Vandamme & Walter & Watanabe & Wuyts & Felis & Gänzle & Lebeer 2020, COMB. NOV.
Creators: name: Zheng, Jinshui
name: Wittouck, Stijn
name: Salvetti, Elisa
name: Franz, Charles M. A. P.
name: Harris, Hugh M. B.
name: Mattarelli, Paola
name: O'Toole, Paul W.
name: Pot, Bruno
name: Vandamme, Peter
name: Walter, Jens
name: Watanabe, Koichi
name: Wuyts, Sander
name: Felis, Giovanna E.
name: Gänzle, Michael G.
name: Lebeer, Sarah
Publisher: name: Zenodo
Year: 2020
Subjects: Biodiversity
Taxonomy
Bacteria
Firmicutes
Bacilli
Lactobacillales
Lactobacillaceae
Lentilactobacillus
Lentilactobacillus rapi

description: DESCRIPTION OF LENTILACTOBACILLUS RAPI COMB. NOV.
Lentilactobacillus rapi (ra’pi. L. gen. n. rapi of a turnip, the substrate for fermented sunki products).
Basonym: Lactobacillus rapi Watanabe et al. 2009, 759 VP
Origin and physiological properties are similar to L. kisonensis [333]. The genome size of the type strain is 2.86 Mbp. The mol% G+C content of DNA is 43.0.
Isolated from sunki and other vegetable fermentations.Thetypestrainis
YIT 11204 T =DSM 19907 T =JCM15042T=NRIC 0743T.
Genome sequence accession number: AZEI00000000.
16S rRNA gene accession number: AB366389.
description: Published as part of Zheng, Jinshui, Wittouck, Stijn, Salvetti, Elisa, Franz, Charles M. A. P., Harris, Hugh M. B., Mattarelli, Paola, O'Toole, Paul W., Pot, Bruno, Vandamme, Peter, Walter, Jens, Watanabe, Koichi, Wuyts, Sander, Felis, Giovanna E., Gänzle, Michael G. & Lebeer, Sarah, 2020, A taxonomic note on the genus Lactobacillus: Description of 23 novel genera, emended description of the genus Lactobacillus Beijerinck 1901, and union of Lactobacillaceae and Leuconostocaceae, pp. 2782-2858 in International Journal of Systematic and Evolutionary Microbiology 70 on page 2846, DOI: 10.1099/ijsem.0.004107, http://zenodo.org/record/4730536
Mus baoulei
Creators: name: Musser, Guy G.
name: Carleton, Michael D.
Publisher: name: Zenodo
Year: 1993
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Mammalia
Rodentia
Muridae
Mus
Mus baoulei

description: Mus baoulei (Vermeiren and Verheyen, 1980). Rev. Zool. Afr., 94:573. TYPE LOCALITY: Ivory Coast, Lamto. DISTRIBUTION: Known only from Ivory Coast and E Guinea. COMMENTS: Subgenus Nannomys. A species occurring sympatrically with M. musculoides and M. setulosus , and whose morphology is closely similar to those in the M. sorella group (Vermeiren and Verheyen, 1980). The diagnostic traits reported for M. baoulei by Vermeiren and Verheyen (1980) are those that set M. sorella apart from other species of Mus (Verheyen, 1965«). Judged by their description, baoulei is distinguished from M. sorella by smaller size, a contrast that also exists between M. sorella and M. neavei (see that account). The relationship of baoulei to other members of the M. sorella group requires fresh assessment.
description: Published as part of Guy G. Musser & Michael D. Carleton, 1993, Order Rodentia - Family Muridae, pp. 501-755 in Mammal Species of the World (2 nd Edition), Washington and London :Smithsonian Institution Press on page 622, DOI: 10.5281/zenodo.7353098
description: {"references": ["Vermeiren, L., and W. N. Verheyen. 1980. Notes sur les Leggada de Lamto, Cote d'Ivoire, avec la description de Leggada baoulei sp. n. (Mammalia, Muridae). Revue de Zoologie Africaine, 94: 570 - 590."]}
The likely Fermi Detection of the Supernova Remnant RCW 103
Creators: name: Xing, Yi
name: Wang, Zhongxiang
name: Zhang, Xiao
name: Chen, Yang
Publisher: name: arXiv
Year: 2013
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: We report on the results from our $γ$-ray analysis of the supernova remnant (SNR) RCW 103 region. The data were taken with the Large Area Telescope on board the Fermi Gamma-ray Space Telescope. An extended source is found at a position consistent with that of RCW 103, and its emission was only detected above 1 GeV (10$σ$ significance), having a power-law spectrum with a photon index of 2.0$\pm$0.1. We obtain its 1--300 GeV spectrum, and the total flux gives a luminosity of 8.3$\times 10^{33}$ erg s$^{-1}$ at a source distance of 3.3 kpc. Given the positional coincidence and property similarities of this source with other SNRs, we identify it as the likely Fermi $γ$-ray counterpart to RCW 103. Including radio measurements of RCW 103, the spectral energy distribution (SED) is modeled by considering emission mechanisms based on both hadronic and leptonic scenarios. We find that models in the two scenarios can reproduce the observed SED, while in the hadronic scenario the existence of SNR--molecular-cloud interaction is suggested as a high density of the target protons is required.
description: 6 pages, 3 figures, accepted for publication in ApJ
Trapping light by mimicking gravitational lensing
Creators: name: Sheng, C.
name: Liu, H.
name: Wang, Y.
name: Zhu, S. N.
name: Genov, D. A.
Publisher: name: arXiv
Year: 2013
Subjects: subject: Optics (physics.optics)
subject: Space Physics (physics.space-ph)
subject: FOS: Physical sciences

description: One of the most fascinating predictions of the theory of general relativity is the effect of gravitational lensing, the bending of light in close proximity to massive stellar objects. Recently, artificial optical materials have been proposed to study the various aspects of curved spacetimes, including light trapping and Hawking's radiation. However, the development of experimental toy models that simulate gravitational lensing in curved spacetimes remains a challenge, especially for visible light. Here, by utilizing a microstructured optical waveguide around a microsphere, we propose to mimic curved spacetimes caused by gravity, with high precision. We experimentally demonstrate both far-field gravitational lensing effects and the critical phenomenon in close proximity to the photon sphere of astrophysical objects under hydrostatic equilibrium. The proposed microstructured waveguide can be used as an omnidirectional absorber, with potential light harvesting and microcavity applications.
description: 17 pages, 4 figures. This work is published at Nature Photonics, Published online: 29 September 2013
Numerical analysis of detection-mechanism models of SNSPD
Creators: name: Engel, Andreas
name: Schilling, Andreas
Publisher: name: arXiv
Year: 2013
Subjects: subject: Superconductivity (cond-mat.supr-con)
subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Instrumentation and Detectors (physics.ins-det)
subject: FOS: Physical sciences

description: The microscopic mechanism of photon detection in superconducting nanowire single-photon detectors is still under debate. We present a simple, but powerful theoretical model that allows us to identify essential differences between competing detection mechanisms. The model is based on quasi-particle multiplication and diffusion after the absorption of a photon. We then use the calculated spatial and temporal evolution of this quasi-particle cloud to determine detection criteria of three distinct detection mechanisms, based on the formation of a normal conducting spot, the reduction of the effective depairing critical current below the bias current and a vortex-crossing scenario, respectively. All our calculations as well as a comparison to experimental data strongly support the vortex-crossing detection mechanism by which vortices and antivortices enter the superconducting strip from the edges and subsequently traverse it thereby triggering the detectable normal conducting domain. These results may therefore help to reveal the microscopic mechanism responsible for the detection of photons in superconducting nanowires.
description: 13 pages, 10 figures submitted to J. Appl. Phys revised manuscript contains an additional table and some corrections
Conceptional Design of the Laser Ion Source based Hadrontherapy Facility
Creators: name: Xie, Xiucui
name: Song, Mingtao
name: Zhang, Xiaohu
Publisher: name: arXiv
Year: 2013
Subjects: subject: Accelerator Physics (physics.acc-ph)
subject: FOS: Physical sciences

description: Laser ion source (LIS), which can provide carbon beam with highly stripped state (C6+) and high intensity (several tens mA), would significantly change the overall design of the hadrontherapy facility. A LIS based hadrontherapy facility is proposed with the advantage of short linac length, simple injection scheme and small synchrotron size. With the experience from the DPIS and HITFiL project that had conducted in IMP, a conceptional design of the LIS based hadrontherapy facility will be present with special dedication to APF type IH DTL design and simulation.
description: 5 pages, submitted to Chinese Physics C
Additional file 1 of Thymofibrolipoma: a case report and review of the literature
Creators: name: Jokoji, Ryu
name: Tomita, Emiko
Publisher: name: figshare
Year: 2022
Subjects: subject: Space Science
subject: Medicine
subject: Cell Biology
subject: Molecular Biology
subject: Biotechnology
subject: Immunology
subject: FOS: Clinical medicine
subject: Cancer
subject: Plant Biology
subject: FOS: Biological sciences
subject: Computational Biology

description: Supplementary Material 1
Additional file 1 of Analysis of gene expression levels and their impact on survival in 31 cancer-types patients identifies novel prognostic markers and suggests unexplored immunotherapy treatment options in a wide range of malignancies
Creators: name: Giampietri, Claudia
name: Scatozza, Francesca
name: Crecca, Elena
name: Vigiano Benedetti, Virginia
name: Natali, Pier Giorgio
name: Facchiano, Antonio
Publisher: name: figshare
Year: 2022
Subjects: subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Immunology
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: Cancer

description: Additional file 1. Supplemental material.
Mus booduga
Creators: name: Musser, Guy G.
name: Carleton, Michael D.
Publisher: name: Zenodo
Year: 1993
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Mammalia
Rodentia
Muridae
Mus
Mus booduga

description: Mus booduga (Gray, 1837). Mag. Nat. Hist. [Charlesworth's], 1:586. TYPE LOCALITY: India, S Mahratta. DISTRIBUTION: Sri Lanka, Peninsular India (north to Jammu and Kashmir), S Nepal, and C Burma. COMMENTS: Subgenus Mus. Results from chromosomal analyses reported by Sen and Sharma (1983) and Sharma et al. (1986) in context of evolutionary divergence relative to other species of Mus.
description: Published as part of Guy G. Musser & Michael D. Carleton, 1993, Order Rodentia - Family Muridae, pp. 501-755 in Mammal Species of the World (2 nd Edition), Washington and London :Smithsonian Institution Press on page 622, DOI: 10.5281/zenodo.7353098
description: {"references": ["Sen, S., and T. Sharma. 1983. Role of constitutive heterochromatin in evolutionary divergence: Results of chromosome banding and condensation inhibition studies in Mus musculus, Mus booduga and Mus dunni. Evolution, 37: 628 - 636.", "Sharma, T., N. Cheong, P. Sen, and S. Sen. 1986. Constitutive heterochromatin and evolutionary divergence of Mus dunni, M. booduga and M. musculus. Pp. 35 - 44, in Current topics in microbioloby and immunology, vol. 127 (M. Potter, J. H. Nadeau, and M. P. Cancro, eds.). Springer-Verlag, Berlin, 395 pp."]}
Lentilactobacillus senioris Zheng & Wittouck & Salvetti & Franz & Harris & Mattarelli & O'Toole & Pot & Vandamme & Walter & Watanabe & Wuyts & Felis & Gänzle & Lebeer 2020, COMB. NOV.
Creators: name: Zheng, Jinshui
name: Wittouck, Stijn
name: Salvetti, Elisa
name: Franz, Charles M. A. P.
name: Harris, Hugh M. B.
name: Mattarelli, Paola
name: O'Toole, Paul W.
name: Pot, Bruno
name: Vandamme, Peter
name: Walter, Jens
name: Watanabe, Koichi
name: Wuyts, Sander
name: Felis, Giovanna E.
name: Gänzle, Michael G.
name: Lebeer, Sarah
Publisher: name: Zenodo
Year: 2020
Subjects: Biodiversity
Taxonomy
Bacteria
Firmicutes
Bacilli
Lactobacillales
Lactobacillaceae
Lentilactobacillus
Lentilactobacillus senioris

description: DESCRIPTIONOF LENTILACTOBACILLUS SENIORIS COMB. NOV.
Lentilactobacillus senioris (se.ni.o’ris. L. gen. n. senioris of an elderly person, indicating the source of the type strain).
Basonym: Lactobacillus senioris Oki et al., 2012, 606 VP
Growth is observed at 15 and 37 °C but not at 45 °C; the type strain was isolated from humanfaeces [173]. L. senioris is the most distantly related member of the genus, has the smallest genome size (1.57 Mbp) and lowest G+C content (39.9) among species in the genus, and does not share the signature genes that are shared by other lentilactobacilli, which may indicate that L. senioris transitions from a free-living to a host-adapted lifestyle.
Isolated from from the faeces of a 100-year-old female.
Thetypestrainis YIT 12364 T =DSM 24302 T =JCM 17472 T.
Genome sequence accession number: AYZR00000000.
16S rRNA gene accession number: AB602570.
description: Published as part of Zheng, Jinshui, Wittouck, Stijn, Salvetti, Elisa, Franz, Charles M. A. P., Harris, Hugh M. B., Mattarelli, Paola, O'Toole, Paul W., Pot, Bruno, Vandamme, Peter, Walter, Jens, Watanabe, Koichi, Wuyts, Sander, Felis, Giovanna E., Gänzle, Michael G. & Lebeer, Sarah, 2020, A taxonomic note on the genus Lactobacillus: Description of 23 novel genera, emended description of the genus Lactobacillus Beijerinck 1901, and union of Lactobacillaceae and Leuconostocaceae, pp. 2782-2858 in International Journal of Systematic and Evolutionary Microbiology 70 on page 2846, DOI: 10.1099/ijsem.0.004107, http://zenodo.org/record/4730536
Event-Driven Contrastive Divergence for Spiking Neuromorphic Systems
Creators: name: Neftci, Emre
name: Das, Srinjoy
name: Pedroni, Bruno
name: Kreutz-Delgado, Kenneth
name: Cauwenberghs, Gert
Publisher: name: arXiv
Year: 2013
Subjects: subject: Neural and Evolutionary Computing (cs.NE)
subject: Neurons and Cognition (q-bio.NC)
subject: FOS: Computer and information sciences
subject: FOS: Biological sciences

description: Restricted Boltzmann Machines (RBMs) and Deep Belief Networks have been demonstrated to perform efficiently in a variety of applications, such as dimensionality reduction, feature learning, and classification. Their implementation on neuromorphic hardware platforms emulating large-scale networks of spiking neurons can have significant advantages from the perspectives of scalability, power dissipation and real-time interfacing with the environment. However the traditional RBM architecture and the commonly used training algorithm known as Contrastive Divergence (CD) are based on discrete updates and exact arithmetics which do not directly map onto a dynamical neural substrate. Here, we present an event-driven variation of CD to train a RBM constructed with Integrate & Fire (I&F) neurons, that is constrained by the limitations of existing and near future neuromorphic hardware platforms. Our strategy is based on neural sampling, which allows us to synthesize a spiking neural network that samples from a target Boltzmann distribution. The recurrent activity of the network replaces the discrete steps of the CD algorithm, while Spike Time Dependent Plasticity (STDP) carries out the weight updates in an online, asynchronous fashion. We demonstrate our approach by training an RBM composed of leaky I&F neurons with STDP synapses to learn a generative model of the MNIST hand-written digit dataset, and by testing it in recognition, generation and cue integration tasks. Our results contribute to a machine learning-driven approach for synthesizing networks of spiking neurons capable of carrying out practical, high-level functionality.
description: (Under review)
title: Automated Sleep Scoring, Deep Learning and Physician Supervision
Creators: name: Fiorillo, Luigi
Publisher: name: Universität Bern
Year: 2023
Subjects: subject: 000 Computer science, knowledge & systems
subject: 610 Medicine & health

description: Sleep plays a crucial role in human well-being. Polysomnography is used in sleep medicine as a diagnostic tool, so as to objectively analyze the quality of sleep. Sleep scoring is the procedure of extracting sleep cycle information from the whole-night electrophysiological signals. The scoring is done worldwide by the sleep physicians according to the official American Academy of Sleep Medicine (AASM) scoring manual. In the last decades, a wide variety of deep learning based algorithms have been proposed to automatise the sleep scoring task. In this thesis we study the reasons why these algorithms fail to be introduced in the daily clinical routine, with the perspective of bridging the existing gap between the automatic sleep scoring models and the sleep physicians. In this light, the primary step is the design of a simplified sleep scoring architecture, also providing an estimate of the model uncertainty. Beside achieving results on par with most up-to-date scoring systems, we demonstrate the efficiency of ensemble learning based algorithms, together with label smoothing techniques, in both enhancing the performance and calibrating the simplified scoring model. We introduced an uncertainty estimate procedure, so as to identify the most challenging sleep stage predictions, and to quantify the disagreement between the predictions given by the model and the annotation given by the physicians. In this thesis we also propose a novel method to integrate the inter-scorer variability into the training procedure of a sleep scoring model. We clearly show that a deep learning model is able to encode this variability, so as to better adapt to the consensus of a group of scorers-physicians. We finally address the generalization ability of a deep learning based sleep scoring system, further studying its resilience to the sleep complexity and to the AASM scoring rules. We can state that there is no need to train the algorithm strictly following the AASM guidelines. Most importantly, using data from multiple data centers results in a better performing model compared with training on a single data cohort. The variability among different scorers and data centers needs to be taken into account, more than the variability among sleep disorders.
Mus bufo
Creators: name: Musser, Guy G.
name: Carleton, Michael D.
Publisher: name: Zenodo
Year: 1993
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Mammalia
Rodentia
Muridae
Mus
Mus bufo

description: Mus bufo (Thomas, 1906). Ann. Mag. Nat. Hist., ser. 7, 18: 145. TYPE LOCALITY: Uganda, Ruwenzori East, 6000 ft. DISTRIBUTION: E Zaire (Kivu region), adjacent Uganda, Rwanda, and Burundi; a montane Western Rift endemic. SYNONYMS: ablutus, wambutti. COMMENTS: Subgenus Nannomys. In body size and morphology, M. bufo superficially resembles the large-bodied M. triton , but the two are distinguished by dental features and tail length (Petter and Matthey, 1975) as well as karyotypes (Robbins and Baker, 1978), and both occur together in the Kivu region of E Zaire (specimens in the American Museum of Natural History). Chromosomal data for Burundi samples reported by Maddalena et al. (1989).
description: Published as part of Guy G. Musser & Michael D. Carleton, 1993, Order Rodentia - Family Muridae, pp. 501-755 in Mammal Species of the World (2 nd Edition), Washington and London :Smithsonian Institution Press on page 622, DOI: 10.5281/zenodo.7353098
description: {"references": ["Petter, F., and R. Matthey. 1975. Genus Mus, Part 6.7. Pp. 1 - 4, in The mammals of Africa: An identification manual (J. Meester and H. W. Setzer, eds.),. Smithsonian Institution Press, Washington, D. C., not continuously paginated.", "Robbins, L. W., and R. J. Baker. 1978. Karyotypic data for African mammals, with a description of an in vivo bone marrow technique. Bulletin of the Carnegie Museum of Natural History, 6: 188 - 210.", "Maddalena, T., E. Van der Straeten, L. Ntahuga, and A. Sparti. 1989. Nouvelles donnees et caryotypes des rongeurs du Burundi. Revue Suisse de Zoologie, 96: 939 - 948."]}
On periodically driven AdS/CFT
Creators: name: Auzzi, Roberto
name: Elitzur, Shmuel
name: Gudnason, Sven Bjarke
name: Rabinovici, Eliezer
Publisher: name: arXiv
Year: 2013
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: We use the AdS/CFT correspondence to study a thermally isolated conformal field theory in four dimensions which undergoes a repeated deformation by an external periodic time-dependent source coupled to an operator of dimension Delta. The initial state of the theory is taken to be at a finite temperature. We compute the energy dissipated in the system as a function of the frequency and of the dimension Delta of the perturbing operator. This is done in the linear response regime. In order to study the details of thermalization in the dual field theory, the leading-order backreaction on the AdS black brane metric is computed. The evolution of the event and the apparent horizons is monitored; the increase of area in each cycle coincides with the increase in the equilibrium entropy corresponding to the amount of energy dissipated. The time evolution of the entanglement entropy of a spherical region and that of the two-points function of a probe operator with a large dimension are also inspected; we find a delay in the thermalization of these quantities which is proportional to the size of the region which is being probed. Thus, the delay is more pronounced in the infrared. We comment on a possible transition in the time evolution of the energy fluctuations.
description: 44 pages, 35 figures; V2: corrected typos
Additional file 2 of A multi-omics approach unravels metagenomic and metabolic alterations of a probiotic and synbiotic additive in rainbow trout (Oncorhynchus mykiss)
Creators: name: Rasmussen, Jacob Agerbo
name: Villumsen, Kasper Rømer
name: Ernst, Madeleine
name: Hansen, Martin
name: Forberg, Torunn
name: Gopalakrishnan, Shyam
name: Gilbert, M. Thomas P.
name: Bojesen, Anders Miki
name: Kristiansen, Karsten
name: Limborg, Morten Tønsberg
Publisher: name: figshare
Year: 2022
Subjects: subject: Microbiology
subject: FOS: Biological sciences

description: Additional file 1 Supplementary information.
The Origin of Galactic Cosmic Rays
Creators: name: Blasi, Pasquale
Publisher: name: arXiv
Year: 2013
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: One century ago Viktor Hess carried out several balloon flights that led him to conclude that the penetrating radiation responsible for the discharge of electroscopes was of extraterrestrial origin. One century from the discovery of this phenomenon seems to be a good time to stop and think about what we have understood about Cosmic Rays. The aim of this review is to illustrate the ideas that have been and are being explored in order to account for the observable quantities related to cosmic rays and to summarize the numerous new pieces of observation that are becoming available. In fact, despite the possible impression that development in this field is somewhat slow, the rate of new discoveries in the last decade or so has been impressive, and mainly driven by beautiful pieces of observation. At the same time scientists in this field have been able to propose new, fascinating ways to investigate particle acceleration inside the sources, making use of multifrequency observations that range from the radio, to the optical, to X-rays and gamma rays. These ideas can now be confronted with data. I will mostly focus on supernova remnants as the most plausible sources of Galactic cosmic rays, and I will review the main aspects of the modern theory of diffusive particle acceleration at supernova remnant shocks, with special attention for the dynamical reaction of accelerated particles on the shock and the phenomenon of magnetic field amplification at the shock. Cosmic ray escape from the sources is discussed as a necessary step to determine the spectrum of cosmic rays at the Earth. In the end of this review I will also discuss the phenomenon of cosmic ray acceleration at shocks propagating in partially ionized media and the implications of this phenomenon in terms of width of the Balmer line emission.
description: 88 Pages, Review paper to appear in A&A Reviews - A typo corrected
Efficient Estimation of Highly Structured Posteriors of Gravitational-Wave Signals with Markov-Chain Monte Carlo
Creators: name: Farr, Benjamin
name: Kalogera, Vicky
name: Luijten, Erik
Publisher: name: arXiv
Year: 2013
Subjects: subject: Instrumentation and Methods for Astrophysics (astro-ph.IM)
subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: We introduce a new Markov-Chain Monte Carlo (MCMC) approach designed for efficient sampling of highly correlated and multimodal posteriors. Parallel tempering, though effective, is a costly technique for sampling such posteriors. Our approach minimizes the use of parallel tempering, only using it for a short time to tune a new jump proposal. For complex posteriors we find efficiency improvements up to a factor of ~13. The estimation of parameters of gravitational-wave signals measured by ground-based detectors is currently done through Bayesian inference with MCMC one of the leading sampling methods. Posteriors for these signals are typically multimodal with strong non-linear correlations, making sampling difficult. As we enter the advanced-detector era, improved sensitivities and wider bandwidths will drastically increase the computational cost of analyses, demanding more efficient search algorithms to meet these challenges.
title: Основные категории, ориентированные на выражение грамматических отношений в английском, немецком и французском языках
Creators: name: ELS IPR BOOKS
Publisher: name: Донской государственный технический университет
Year: 2019

description: Содержит основной теоретический материал по грамматике английского, немецкого и французского языков, построенный по единой схеме и направленный на формирование у слушателей базовых компетенций и навыков владения и распознавания иностранной речи. Текст излагается на русском языке с примерами на иностранном, что способствует более глубокому и детальному пониманию слушателями изучаемого материала. Предназначено для студентов первого курса всех направлений подготовки заочной формы обучения.
TRIGONOMETRIK IFODALARNI AYNIY ALMASHTIRISH MAVZUSINING DOLZARBLIGI
Creators: name: Sabirova, Gulidonaxon
Publisher: name: Zenodo
Year: 2023

description: Maqolada trіgonometrіk іfodalarnі almashtіrіshga doіr mіsollar, formulalar, yo`l-yo`rіqlar ko`rsatіb berіladі. XXІ asr іnformatsіon texnologіyalar asrі bo`lganlіgі boіs matematіkanіng har bіr darsі o`quvchі uchun dolzarb hіsoblanadі.
Signal and response properties indicate an optoacoustic effect underlying the intra-cochlear laser-optical stimulation
Creators: name: Kallweit, Nicole
name: Baumhoff, Peter
name: Krueger, Alexander
name: Tinne, Nadine
name: Heisterkamp, Alexander
name: Kral, Andrej
name: Maier, Hannes
name: Ripken, Tammo
Publisher: name: Bellingham, WA : S P I E - International Society for Optical Engineering
Year: 2016
Subjects: subject: Pulsed laser operation
subject: In vivo imaging
subject: Signal detection
subject: Absorption
subject: Laser systems engineering
subject: Infrared radiation
subject: Sensors
subject: Konferenzschrift
subject: Dewey Decimal Classification::600 | Technik::620 | Ingenieurwissenschaften und Maschinenbau

description: Optical cochlea stimulation is under investigation as a potential alternative to conventional electric cochlea implants in treatment of sensorineural hearing loss. If direct optical stimulation of spiral ganglion neurons (SGNs) would be feasible, a smaller stimulation volume and, therefore, an improved frequency resolution could be achieved. However, it is unclear whether the mechanism of optical stimulation is based on direct neuronal stimulation or on optoacoustics. Animal studies on hearing vs. deafened guinea pigs already identified the optoacoustic effect as potential mechanism for intra-cochlear optical stimulation. In order to characterize the optoacoustic stimulus more thoroughly the acoustic signal along the beam path of a pulsed laser in water was quantified and compared to the neuronal response properties of hearing guinea pigs stimulated with the same laser parameters. Two pulsed laser systems were used for analyzing the influence of variable pulse duration, pulse energy, pulse peak power and absorption coefficient. Preliminary results of the experiments in water and in vivo suggesta similar dependency of response signals on the applied laser parameters: Both datasets show an onset and offset signal at the beginning and the end of the laser pulse. Further, the resulting signal amplitude depends on the pulse peak power as well as the temporal development of the applied laser pulse. The data indicates the maximum of the first derivative of power as the decisive factor. In conclusion our findings strengthen the hypothesis of optoacoustics as the underlying mechanism for optical stimulation of the cochlea. © SPIE 2016
Mus callewaerti
Creators: name: Musser, Guy G.
name: Carleton, Michael D.
Publisher: name: Zenodo
Year: 1993
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Mammalia
Rodentia
Muridae
Mus
Mus callewaerti

description: Mus callewaerti (Thomas, 1925). Ann. Mag. Nat. Hist., ser. 9, 15:668. TYPE LOCALITY: S Zaire, Lualaba, Luluabourg, 610 m. DISTRIBUTION: Recorded only from N and C Angola, S and W Zaire; limits unknown. COMMENTS: Subgenus Nannomys. Thomas described this species as a member of the genus Hylenomys, which is now united with Mus (Hill and Carter, 1941; Misonne, 1965). It is the largest-bodied of any of the African Mus (Petter and Matthey, 1975), has ivory incisors and very large auditory bullae, and in external features resembles M. triton , which misled Hatt (1940«) into treating callewaerti as a subspecies of triton. Misonne (1965) summarized distributional and other information.
description: Published as part of Guy G. Musser & Michael D. Carleton, 1993, Order Rodentia - Family Muridae, pp. 501-755 in Mammal Species of the World (2 nd Edition), Washington and London :Smithsonian Institution Press on page 622, DOI: 10.5281/zenodo.7353098
description: {"references": ["Hill, J. E., and T. D. Carter. 1941. The mammals of Angola, Africa. Bulletin of the American Museum of Natural History, 78 (1): 1 - 211.", "Petter, F., and R. Matthey. 1975. Genus Mus, Part 6.7. Pp. 1 - 4, in The mammals of Africa: An identification manual (J. Meester and H. W. Setzer, eds.),. Smithsonian Institution Press, Washington, D. C., not continuously paginated."]}
Lentilactobacillus sunkii SUNKII 2020, COMB. NOV.
Creators: name: Zheng, Jinshui
name: Wittouck, Stijn
name: Salvetti, Elisa
name: Franz, Charles M. A. P.
name: Harris, Hugh M. B.
name: Mattarelli, Paola
name: O'Toole, Paul W.
name: Pot, Bruno
name: Vandamme, Peter
name: Walter, Jens
name: Watanabe, Koichi
name: Wuyts, Sander
name: Felis, Giovanna E.
name: Gänzle, Michael G.
name: Lebeer, Sarah
Publisher: name: Zenodo
Year: 2020
Subjects: Biodiversity
Taxonomy
Bacteria
Firmicutes
Bacilli
Lactobacillales
Lactobacillaceae
Lentilactobacillus
Lentilactobacillus sunkii

description: DESCRIPTIONOF LENTILACTOBACILLUS SUNKII COMB. NOV.
Lentilactobacillus sunkii (sun’ki.i. N.L. gen. n. sunkii of sunki, non-salted Japanese traditional pickle).
Basonym: Lactobacillus sunkii Watanabe et al. 2009, 759 VP
Physiological properties and origin are comparable to L. kisonensis [333]. The genome size of the type strain is 2.69 Mbp. The mol% G+C content of DNA is 42.1.
Isolated from sunki, a fermented turnip product, and from kefir.Thetypestrainis
YIT 11161 T =DSM 19904 T =JCM15039T=NRIC 0744T.
Genome sequence accession number: AZEA00000000.mol% G+C content of DNAis 36.9.
description: Published as part of Zheng, Jinshui, Wittouck, Stijn, Salvetti, Elisa, Franz, Charles M. A. P., Harris, Hugh M. B., Mattarelli, Paola, O'Toole, Paul W., Pot, Bruno, Vandamme, Peter, Walter, Jens, Watanabe, Koichi, Wuyts, Sander, Felis, Giovanna E., Gänzle, Michael G. & Lebeer, Sarah, 2020, A taxonomic note on the genus Lactobacillus: Description of 23 novel genera, emended description of the genus Lactobacillus Beijerinck 1901, and union of Lactobacillaceae and Leuconostocaceae, pp. 2782-2858 in International Journal of Systematic and Evolutionary Microbiology 70 on page 2847, DOI: 10.1099/ijsem.0.004107, http://zenodo.org/record/4730536
Three-dimensional imaging of intracochlear tissue by scanning laser optical tomography (SLOT)
Creators: name: Tinne, N.
name: Nolte, L.
name: Antonopoulos, Georgios C.
name: Schulze, J.
name: Andrade, J.
name: Heisterkamp, A.
name: Meyer, H.
name: Warnecke, A.
name: Majdani, Omid
name: Ripken, T.
Publisher: name: Bellingham, WA : S P I E - International Society for Optical Engineering
Year: 2016
Subjects: subject: 3D microscopy
subject: antibody staining
subject: cochlea
subject: inner ear
subject: optical clearing
subject: scanning laser optical tomography
subject: SLOT
subject: tomography
subject: ?CT
subject: Antibodies
subject: Fluorescence
subject: Optical tomography
subject: Scanning
subject: Tissue
subject: Tomography
subject: Visualization
subject: 3-D microscopy
subject: Inner ear
subject: Optical clearing
subject: Scanning lasers
subject: Computerized tomography
subject: Konferenzschrift
subject: Dewey Decimal Classification::600 | Technik::620 | Ingenieurwissenschaften und Maschinenbau

description: The presented study focuses on the application of scanning laser optical tomography (SLOT) for non-destructive visualization of anatomical structures inside the human cochlea ex vivo. SLOT is a laser-based highly efficient microscopy technique, which allows for tomographic imaging of the internal structure of transparent large-scale specimens (up to 1 cm3). Thus, in the field of otology this technique is best convenient for an ex vivo study of the inner ear anatomy. For this purpose, the preparation before imaging comprises mechanically assisted decalcification, dehydration as well as optical clearing of the cochlea samples. Here, we demonstrate results of SLOT visualizing hard and soft tissue structures of the human cochlea with an optical resolution in the micrometer range using absorption and autofluorescence as contrast mechanisms. Furthermore, we compare our results with the method of X-ray micro tomography (micro-CT, μCT) as clinical gold standard which is based only on absorption. In general, SLOT can provide the advantage of covering all contrast mechanisms known from other light microscopy techniques, such as fluorescence or scattering. For this reason, a protocol for antibody staining has been developed, which additionally enables selective mapping of cellular structures within the cochlea. Thus, we present results of SLOT imaging rodent cochleae showing specific anatomical structures such as hair cells and neurofilament via fluorescence. In conclusion, the presented study has shown that SLOT is an ideally suited tool in the field of otology for in toto visualization of the inner ear microstructure. © 2016 SPIE.
Additional file 2 of Southern Carpathian ultramafic grasslands within the central-southeast European context: syntaxonomic classification and overall eco-coenotic patterns
Creators: name: Coldea, Gheorghe
name: Gafta, Dan
name: Negrean, Gavril
name: Stoica, Adrian Ilie
name: Hurdu, Bogdan-Iuliu
Publisher: name: figshare
Year: 2022
Subjects: subject: Ecology
subject: FOS: Biological sciences

description: Additional file 2: Appendix S2. Photos of the studied serpentine vegetation in the South-Eastern Carpathians (Romania). (A) Thermophilous phytocoenosis from the Mehedinți Plateau, with Asplenium serpentini and Notholaena marantae (photo: I. Ciortan, 04.07.2017). (B) and (C) Typical serpentine plant species from the Mehedinți Mts., showing Plantago serpentina and respectively, Armeria halleri (photo: I. Ciortan, 05.07.2017). (D) Open communities dominated by Plantago holosteum, Anthemis cretica subsp. kitaibelii and Minuartia frutescens on antigorite-rich rocks from the northern Retezat Mts., Poieni Peak—Ohaba de sub Piatră (photo: M. Ciobanu, 21.07.2017). (E) Phytocoenosis featuring Plantago holosteum, Brukenthalia spiculifolia and Anthemis carpatica from the Cozia Mts. (photo: P.M. Szatmari, 19.07.2017).
Mus caroli Bonhote 1902
Creators: name: Musser, Guy G.
name: Carleton, Michael D.
Publisher: name: Zenodo
Year: 1993
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Mammalia
Rodentia
Muridae
Mus
Mus caroli

description: Mus caroli Bonhote, 1902. Novit. Zool., 9:627. TYPE LOCALITY: Japan, Ryukyu (= Liukiu) Isis, Okinawa Isl. DISTRIBUTION: Natural range probably from Ryukyu Isis to Taiwan, S China (Fujian and Yunnan Provs., Hainan Isl, Hong Kong), Vietnam, Laos, Cambodia, and Thailand (N of Isthmus of Kra; see map in J. T. Marshall, Jr., 1977a). Also recorded from Malay Peninsula (S Kedah State), Sumatra, Java, Madura, and Flores Isis in Nusa Tenggara, all places where it was likely inadvertently introduced (Musser and Newcomb, 1983). SYNONYMS: boninensis, fornwsanus, kakhyenensis, kukilensis, ouwensi. COMMENTS: Subgenus Mus.
description: Published as part of Guy G. Musser & Michael D. Carleton, 1993, Order Rodentia - Family Muridae, pp. 501-755 in Mammal Species of the World (2 nd Edition), Washington and London :Smithsonian Institution Press on page 623, DOI: 10.5281/zenodo.7353098
description: {"references": ["Musser, G. G., and C. Newcomb. 1983. Malaysian murids and the giant rat of Sumatra. Bulletin of the American Museum of Natural History, 174: 327 - 598."]}
Spin Chaos Manifestation in a Driven Quantum Billiard with Spin-Orbit Coupling
Creators: name: Khomitsky, D. V.
name: Malyshev, A. I.
name: Sherman, E. Ya.
name: Di Ventra, M.
Publisher: name: arXiv
Year: 2013
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Chaotic Dynamics (nlin.CD)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: The coupling of orbital and spin degrees of freedom is the source of many interesting phenomena. Here, we study the electron dynamics in a quantum billiard --a mesoscopic rectangular quantum dot-- with spin-orbit coupling driven by a periodic electric field. We find that both the spatial and temporal profiles of the observables demonstrate the transition to chaotic dynamics with qualitative modifications of the power spectra and patterns of probability and spin density. The time dependence of the wavefunctions and spin density distributions indicates spin-charge separation {seen in the decay of the spin-charge density correlators}. This new spin chaos effect can be experimentally verified leading to a better understanding of the interplay between spin and spatial degrees of freedom, relevant to fundamental and applied quantum physics.
description: 6 pages, 4 figures