cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Monoecocestus threlkeldi
Creators: name: Martins, Natalia Beatriz Guerreiro
name: Robles, María Del Rosario
name: Navone, Graciela Teresa
name: Callejón, Rocío
Publisher: name: Zenodo
Year: 2023
Subjects: Biodiversity
Taxonomy
Animalia
Platyhelminthes
Cestoda
Cyclophyllidea
Anoplocephalidae
Monoecocestus
Monoecocestus threlkeldi

description: Monoecocestus threlkeldi (Parra, 1952)
Description (based on six specimens): strobila total length 0.84 ± 0.05 (0.80–0.87). Scolex 0.17 long by 0.25 wide (Figs. 1a, 2a). Suckers 0.12 ± 0.02 (0.11–0.14) long by 0.11 ± 0.01 (0.10–0.12) wide. Entire worm covered with acicular filitriches (sensu Chervy 2009) (Fig. 2b). Mature proglottids 0.16 ± 0.01 (0.15–0.17) long by 0.84 ± 0.05 (0.80–0.87) wide (Fig. 1b). Genital pores alternate regularly. Testes number 19–20 per proglottid, each testis 0.05 ± 0.01 (0.05–0.06) long by 0.04 ± 0.01 (0.05–0.05) wide. Testes overlap ovary. Cirrus sac 0.13 ± 0.02 (0.11–0.15) long by 0.31 ± 0.05 (0.27–0.36) wide. Cirrus sac crosses osmoregulatory canals, ending near midline of proglottid. Cirrus with spines, usually everted (Fig. 2c–f). Internal seminal vesicle present. Vitellarium 0.14 ± 0.01 (0.13–0.15) wide. Ovary 0.47 ± 0.12 (0.38–0.55) wide. Gravid proglottids 0.78 ± 0.04 (0.75–0.80) long by 1.15 ± 0.08 (1.09–1.12) wide. Eggs 43.6 ± 1.9 (40–45) μm in diameter (Fig. 1c). Embryophore in form of a pyriform apparatus, 21.4 ± 1.8 (19.6–23) μm long. Oncosphere 9.8 ± 1.3 (8–11) μm in diameter.
description: Published as part of Martins, Natalia Beatriz Guerreiro, Robles, María Del Rosario, Navone, Graciela Teresa & Callejón, Rocío, 2023, Monoecocestus (Cestoda: Anoplocephalidae) diversity in Sigmodontinae rodents characterized by morphology and molecular methods, pp. 37-55 in Zootaxa 5380 (1) on page 43, DOI: 10.11646/zootaxa.5380.1.3, http://zenodo.org/record/10212862
Polypedilum arara Bidawid & Fittkau 1995
Creators: name: Zhang, Ruilei
name: Song, Chao
name: Qi, Xin
name: Wang, Xinhua
Publisher: name: Zenodo
Year: 2016
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Diptera
Chironomidae
Polypedilum
Polypedilum arara

description: arara Bidawid & Fittkau, 1995: Entomofauna, 16: 512 (Polypedilum (Tripodura )).
Type locality. Brazil (Mittlerer Amazonas, Santarem).
Distribution. NT: Brazil (Pará, Amazonas).
description: Published as part of Zhang, Ruilei, Song, Chao, Qi, Xin & Wang, Xinhua, 2016, Taxonomic review on the subgenus Tripodura Townes (Diptera: Chironomidae: Polypedilum) from China with eleven new species and a supplementary world checklist, pp. 1-53 in Zootaxa 4136 (1) on page 41, DOI: 10.11646/zootaxa.4136.1.1, http://zenodo.org/record/399782
Bose-Einstein condensation and muon production in ultra-high energy cosmic ray particle collisions
Creators: name: Okorokov, V. A.
Publisher: name: arXiv
Year: 2023
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: Collisions of cosmic ray particles with ultra-high initial energies with nuclei in the atmosphere open a wide room for appearing of the novel dynamical features for multiparticle production processes. In particular, the pion-lasing behavior driven by Bose-Einstein condensation would result in the shift to larger multiplicities and, as consequence, could provide, in general, the enhanced yield of cosmic muons. In the present work the critical value of the space charged particle density for onset of Bose-Einstein condensation of the boson (pion) wave-packets into the same wave-packet state is estimated within the model with complete multiparticle symmetrization for the energy domain corresponded to the ultra-high energy cosmic rays (UHECR). Energy dependence of mean density of charged pions is evaluated for the cases of absent of the Bose-Einstein effects and for presence of laser-like behavior of pions. The possible influence of the Bose-Einstein condensation is discussed for the muon production in UHECR particle collisions with the atmosphere.
description: 13 pages, 4 figures. 4th International symposium on cosmic rays and astrophysics (ISCRA2023). Moscow, Russia, June 27 - 29, 2023
Agnostic detection of large-scale weather patterns in the northern hemisphere: from blockings to teleconnections
Creators: name: Springer, Sebastian
name: Galfi, Vera Melinda
name: Laio, Alessandro
name: Lucarini, Valerio
Publisher: name: arXiv
Year: 2023
Subjects: subject: Atmospheric and Oceanic Physics (physics.ao-ph)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: Data Analysis, Statistics and Probability (physics.data-an)
subject: Geophysics (physics.geo-ph)
subject: FOS: Physical sciences

description: Detecting recurrent weather patterns and understanding the transitions between such regimes are key to advancing our knowledge on the low-frequency variability of the atmosphere and have important implications in terms of weather and climate-related risks. We adapt an analysis pipeline inspired by Markov State Modelling and detect in an unsupervised manner the dominant winter mid-latitude Northern Hemisphere weather patterns in the Atlantic and Pacific sectors. The daily 500 hPa geopotential height fields are first classified in $\sim 200$ microstates. The weather dynamics is then represented in the basis of these microstates and the slowest decaying modes are identified from the spectral properties of the transition probability matrix. These modes are defined on the basis of the nonlinear dynamical processes of the system and not as tentative metastable states as often done in Markov state analysis. In the Atlantic and Pacific sectors slow relaxation processes are mainly related to transitions between blocked regimes and zonal flow. We also find strong evidence of a dynamical regime associated with the simultaneous Atlantic-Pacific blocking. When the analysis is performed in a broader geographical region of the Atlantic sector, we discover that the slowest relaxation modes of the system are associated with transitions between dynamical regimes that resemble teleconnection patterns like the North Atlantic Oscillation and weather regimes like the Scandinavian and Greenland blocking, yet have a much stronger dynamical foundation than classical methods based e.g. on EOF analysis. Our method clarifies that, as a result of the lack of a time-scale separation in the atmospheric variability of the mid-latitudes, there is no clear-cut way to represent the atmospheric dynamics in terms of few, well-defined modes of variability.
description: 32 pages, 4 figures, plus supplementary material. Final accepted version
Monoecocestus undefined-1
Creators: name: Martins, Natalia Beatriz Guerreiro
name: Robles, María Del Rosario
name: Navone, Graciela Teresa
name: Callejón, Rocío
Publisher: name: Zenodo
Year: 2023
Subjects: Biodiversity
Taxonomy
Animalia
Platyhelminthes
Cestoda
Cyclophyllidea
Anoplocephalidae
Monoecocestus
Monoecocestus undefined-1

description: Monoecocestus sp.1
Description (based on two specimens): Scolex 0.10; 0.11 long by 0.14; 0.15 wide (Fig. 1d). Suckers 0.05 ± 0.01 (0.04–0.05) in diameter. Mature proglottids 0.51 ± 0.02 (0.50–0.53) long by 1.70 ± 0.01 (1.60–1.80) wide (Fig. 1e). Genital pores alternate irregularly. Testes number 45 per proglottid, each testis 0.06 ± 0.005 (0.05–0.06) long by 0.03 ± 0.008 (0.03–0.03) wide. Cirrus sac 0.37 long by 0.14 wide. Vitellarium 0.30 ± 0.02 (0.29–0.32) wide. Ovary 0.60 ± 0.01 (0.59–0.61) wide. Gravid proglottids 1.17 ± 0.01 (1.17–1.18) long by 1.85 ± 0.07 (1.79–1.92) wide. Eggs 45.5 ± 4.12 (41–51) μm long by 42.8 ± 3.86 (39–47) μm wide (Fig. 1f). Embryophore in form of a pyriform apparatus.
Taxonomic summary
Host: Holochilus vulpinus
Localities: Estancia San Juan Poriahú, Corrientes Province; Laguna Chascomús, Buenos Aires Province
Voucher specimens: MLP-He 7587, 8033
Comments. The morphological characteristics observed in these specimens allow them to be classified in the genus Monoecocestus i.e., single genitalia; genital pores irregularly alternate; internal and external seminal vesicles present; pyriform apparatus present (Beveridge 1994). Among species with genital pores irregularly alternate, Monoecocestus sp.1 differs from Monoecocestus andersoni Haverkost & Gardner, 2010, Monoecocestus machadoi (Rêgo, 1964), Monoecocestus mackiewiczi Schmidt & Martin, 1978, Monoecocestus microcephalus Haverkost & Gardner, 2010, Monoecocestus minor Rêgo, 1960, M. myopotami and Monoecocestus sininterus Haverkost & Gardner, 2010 by testes number, and from Monoecocestus eljefe Haverkost & Gardner, 2010 and Monoecocestus diplomys Noble & Tesh, 1974 by size of scolex, suckers and eggs.
description: Published as part of Martins, Natalia Beatriz Guerreiro, Robles, María Del Rosario, Navone, Graciela Teresa & Callejón, Rocío, 2023, Monoecocestus (Cestoda: Anoplocephalidae) diversity in Sigmodontinae rodents characterized by morphology and molecular methods, pp. 37-55 in Zootaxa 5380 (1) on pages 44-46, DOI: 10.11646/zootaxa.5380.1.3, http://zenodo.org/record/10212862
Additional file 2: Figure S1. of Insights from the draft genome of the subsection V (Stigonematales) cyanobacterium Hapalosiphon sp. Strain MRB220 associated with 2-MIB production
Creators: name: Boon Tan
name: Te, Shu
name: Chek Boo
name: Gin, Karina
name: Thompson, Janelle
Publisher: name: Figshare
Year: 2016
Subjects: subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Molecular Biology
subject: Biotechnology
subject: Evolutionary Biology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Ecology
subject: 69999 Biological Sciences not elsewhere classified
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Plant Biology
subject: 60506 Virology

description: Neighbor-joining tree of the 16Sâ  23S rRNA internal transcribed spacer of MRB220 and selected gene sequences extracted from sequence genomes of Stigonematales. All sequences were aligned with MUSCLE [49], and alignment column <70Â % identity was stripped using Geneious R7 [50]. Neighbor-joining analysis with 100 bootstrap replicates was conducted using Geneious Tree-builder based on the Tamura-Nei Model. Bootstrap values are labelled in each branch node. (PDF 118Â kb)
Additional file 1: Table S1. of Insights from the draft genome of the subsection V (Stigonematales) cyanobacterium Hapalosiphon sp. Strain MRB220 associated with 2-MIB production
Creators: name: Boon Tan
name: Te, Shu
name: Chek Boo
name: Gin, Karina
name: Thompson, Janelle
Publisher: name: Figshare
Year: 2016
Subjects: subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Biotechnology
subject: Evolutionary Biology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Developmental Biology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: 60506 Virology

description: Average nucleotide identity (ANI) between genome of MRB 220 and those of other Stigonematales. Note: Average nucleotide identity was computed using the JGI IMG pipeline [32]. (DOC 38Â kb)
Polypedilum arua Bidawid-Kafka 1996
Creators: name: Zhang, Ruilei
name: Song, Chao
name: Qi, Xin
name: Wang, Xinhua
Publisher: name: Zenodo
Year: 2016
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Diptera
Chironomidae
Polypedilum
Polypedilum arua

description: arua Bidawid-Kafka, 1996: Entomofauna, 17: 172 (Polypedilum (Tripodura )).
Type locality. Brazil (Rio Itu, Mittlerer Rio Negro).
Distribution. NT: Brazil (Pará, Amazonas, Maranhão).
description: Published as part of Zhang, Ruilei, Song, Chao, Qi, Xin & Wang, Xinhua, 2016, Taxonomic review on the subgenus Tripodura Townes (Diptera: Chironomidae: Polypedilum) from China with eleven new species and a supplementary world checklist, pp. 1-53 in Zootaxa 4136 (1) on page 41, DOI: 10.11646/zootaxa.4136.1.1, http://zenodo.org/record/399782
Additional file 4: Figure S2. of Insights from the draft genome of the subsection V (Stigonematales) cyanobacterium Hapalosiphon sp. Strain MRB220 associated with 2-MIB production
Creators: name: Boon Tan
name: Te, Shu
name: Chek Boo
name: Gin, Karina
name: Thompson, Janelle
Publisher: name: Figshare
Year: 2016
Subjects: subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Molecular Biology
subject: Evolutionary Biology
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: 60506 Virology

description: Sequence alignment of geosmin synthase (geoA) a key enzyme in the pathway for geosmin biosynthesis. Nucleotide alignment was conducted using MUSCLE [49] implemented in Geneious R9 [50]. The height of letters in the sequence logo indicated the degree to which the sequence is conserved. While the annotated geoA sequence from MRB 220 reveals partial nucleotide homology, strictly conserved Mg2+ binding sites at position 90 (DDHFLE) and position 476 (DDYFP) are not shared by MRB 220 indicating the enzyme is likely inactive. (PDF 2328Â kb)
MOESM1 of Factors influencing dropout rate of intermittent preventive treatment of malaria during pregnancy
Creators: name: Doku, David
name: Mumuni Zankawah
name: Addae Adu-Gyamfi
Publisher: name: Figshare
Year: 2016
Subjects: subject: Pharmacology
subject: Biotechnology
subject: Developmental Biology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Computational Biology

description: Additional file 1. Questionnaire, interview and observational guides for data collection on intermittent preventive treatment for malaria dropout rate.
Failure of the Baym-Kadanoff construction to match consistently quantum dynamics with thermodynamic critical behavior
Creators: name: Janiš, Václav
name: Pokorný, Vladislav
name: Kos, Šimon
Publisher: name: arXiv
Year: 2023
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: We disclose a serious deficiency of the Baym-Kadanoff construction of thermodynamically consistent conserving approximations. There are two vertices in this scheme: dynamical and conserving. The divergence of each indicates a phase instability. We show that each leads to incomplete and qualitatively different behavior at different critical points. The diagrammatically controlled dynamical vertex from the Schwinger-Dyson equation does not obey the Ward identity and cannot be continued beyond its singularity. The standardly used dynamical vertex alone cannot, hence, conclusively decide about the stability of the high-temperature phase. On the other hand, the divergence in the conserving vertex, obeying the conservation laws, does not invoke critical behavior of the spectral function and the specific heat. Moreover, the critical behavior of the conserving vertex may become spurious in low-dimensional systems. Consequently, the description of the critical behavior of correlated electrons becomes consistent and reliable only if the fluctuations of the order parameter in the conserving vertex lead to a divergence coinciding with that of the dynamical one.
description: 2nd extended version, 13 pages, 6 figures
Additional file 1: Table S1. of First record of the coloured righteye flounder, Poecilopsetta colorata (Teleostei: Poecilopsettidae) from the Sakalaves seamounts in the Mozambique Channel
Creators: name: Wei-Jen Chen
name: Jhen-Nien Chen
name: Eve-Julie Pernet
name: Olu, Karine
Publisher: name: Figshare
Year: 2016
Subjects: subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Ecology
subject: FOS: Biological sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: Cancer
subject: Inorganic Chemistry
subject: FOS: Chemical sciences
subject: Science Policy

description: List of the samples collected during the cruise (campaign: PAMELA-MOZ01) and examined in this study. CP: Beam trawl. DN: NIWA sledge. DW: WarĂŠn dredge. (DOCX 27 kb)
Palais-Smale sequences for the prescribed Ricci curvature functional
Creators: name: Pulemotov, Artem
name: Ziller, Wolfgang
Publisher: name: arXiv
Year: 2023
Subjects: subject: Differential Geometry (math.DG)
subject: FOS: Mathematics

description: We obtain a complete description of divergent Palais-Smale sequences for the prescribed Ricci curvature functional on compact homogeneous spaces. As an application, we prove the existence of saddle points on generalized Wallach spaces and several types of generalized flag manifolds. We also describe the image of the Ricci map in some of our examples.
description: 34 pages, 10 figures. arXiv admin note: text overlap with arXiv:2110.14129
Additional file 1: of Associations of frailty with health care costs â   results of the ESTHER cohort study
Creators: name: Jens-Oliver Bock
name: Hans-Helmut KĂśnig
name: Brenner, Hermann
name: Haefeli, Walter
name: Quinzler, Renate
name: Matschinger, Herbert
name: Kai-Uwe Saum
name: SchĂśttker, Ben
name: Heider, Dirk
Publisher: name: Figshare
Year: 2016
Subjects: subject: Medicine
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Science Policy

description: Questionnaire. (PDF 93 kb)
On the role of soft gluons in collinear parton densities and parton shower event generators
Creators: name: Mendizabal, M.
name: Guzman, F.
name: Jung, H.
name: Monfared, S. Taheri
Publisher: name: arXiv
Year: 2023
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: The role of soft (non-perturbative) gluons in collinear parton densities and parton shower event generators is investigated with the Parton Branching method as a solution of the DGLAP evolution equations. It is found that soft gluons play a significant role.
 Within the Parton Branching frame, the Sudakov form factor can be split into a perturbative and non-perturbative part. The non-perturbative part can be calculated analytically under certain conditions. It is shown that the inclusion of soft (non-perturbative) gluons in the parton density evolution is essential for the proper cancellation of divergent terms. It is argued that the non-perturbative part of the Sudakov form factor has its correspondence in Transverse Momentum Dependent parton distributions. Within the Parton Branching approach, this non-perturbative Sudakov form factor is constrained by fits of inclusive, collinear parton densities.
 We show that the non-perturbative Sudakov form factor and soft gluon emissions are essential for inclusive distributions (collinear parton densities and Drell-Yan transverse momentum spectra). We also show by using Parton Branching TMD parton shower, that the effect of soft gluons plays essentially no role in final state hadron spectra and jets.
description: Replaced with version published in EPJC
Self-intercalation as origin of high-temperature ferromagnetism in epitaxially grown Fe5GeTe2 thin films
Creators: name: Silinskas, M.
name: Senz, S.
name: Gargiani, P.
name: Ruiz, A. M.
name: Kalkofen, B.
name: Kostanovskiy, I.
name: Mohseni, K.
name: Baldoví, J. J.
name: Meyerheim, H. L.
name: Parkin, S. S. P.
name: Bedoya-Pinto, A.
Publisher: name: arXiv
Year: 2023
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: The role of self-intercalation in 2D van der Waals materials is key to the understanding of many of their properties. Here we show that the magnetic ordering temperature of thin films of the 2D ferromagnet Fe5GeTe2 is substantially increased by self-intercalated Fe that resides in the van der Waals gaps. The epitaxial films were prepared by molecular beam epitaxy and their magnetic properties explored by element-specific x-ray magnetic circular dichroism that showed ferromagnetic ordering up to 375 K. Both surface and bulk sensitive x-ray absorption modes were used to confirm that the magnetic signal is of an intrinsic nature. Fe occupation within the van der Waals gap was determined by x-ray diffraction which showed a notably higher occupation with respect to bulk crystals. We thus infer, supported by first-principles calculations, that the higher magnetic ordering temperature results from an increased exchange interaction between the individual Fe5GeTe2 layers mediated by Fe atoms residing within the van der Waals gaps. Our findings establish self-intercalation during epitaxial growth as an efficient mechanism to achieve high-temperature magnetism in a broad class of van der Waals materials.
description: 10 pages, 3 Figures
Additional file 1: Table S1. of Multi-complexity measures of heart rate variability and the effect of vasopressor titration: a prospective cohort study of patients with septic shock
Creators: name: Brown, Samuel
name: Sorensen, Jeffrey
name: Lanspa, Michael
name: Rondina, Matthew
name: Grissom, Colin
name: Shahul, Sajid
name: V. Mathews
Publisher: name: Figshare
Year: 2016
Subjects: subject: Biochemistry
subject: Space Science
subject: Medicine
subject: Sociology
subject: FOS: Sociology

description: Online Data Supplement. Evaluated complexity measures and association with success of vasopressor titration on univariate and multivariate analyses. (DOCX 30Â kb)
Tracking controllability for the heat equation
Creators: name: Petiso, Jon Asier Bárcena
name: Zuazua, Enrique
Publisher: name: arXiv
Year: 2023
Subjects: subject: Optimization and Control (math.OC)
subject: FOS: Mathematics

description: We study the tracking or sidewise controllability of the heat equation. More precisely, we seek for controls that, acting on part of the boundary of the domain where the heat process evolves, aim to assure that the normal trace or flux on the complementary set tracks a given trajectory. The dual equivalent observability problem is identified. It consists on estimating the boundary sources, localized on a given subset of the boundary, out of boundary measurements on the complementary subset. Classical unique continuation and smoothing properties of the heat equation allow us proving approximate tracking controllability properties and the smoothness of the class of trackable trajectories. We also develop a new transmutation method which allows to transfer known results on the sidewise controllability of the wave equation to the tracking controllability of the heat one. Using the flatness approach we also give explicit estimates on the cost of approximate tracking control. The analysis is complemented with a discussion of some possible variants of these results and a list of open problems.
Polypedilum aruakan Bidawid & Fittkau 1995
Creators: name: Zhang, Ruilei
name: Song, Chao
name: Qi, Xin
name: Wang, Xinhua
Publisher: name: Zenodo
Year: 2016
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Diptera
Chironomidae
Polypedilum
Polypedilum aruakan

description: aruakan Bidawid & Fittkau, 1995: Entomofauna, 16: 494 (Polypedilum (Tripodura )).
Type locality. Brazil (Lago Caldo, unterer Amazonas).
Distribution. NT: Brazil (Amazonas).
description: Published as part of Zhang, Ruilei, Song, Chao, Qi, Xin & Wang, Xinhua, 2016, Taxonomic review on the subgenus Tripodura Townes (Diptera: Chironomidae: Polypedilum) from China with eleven new species and a supplementary world checklist, pp. 1-53 in Zootaxa 4136 (1) on page 41, DOI: 10.11646/zootaxa.4136.1.1, http://zenodo.org/record/399782
Pattern detection in bipartite networks: a review of terminology, applications and methods
Creators: name: Neal, Zachary
name: Cadieux, Annabel
name: Garlaschelli, Diego
name: Gotelli, Nicholas J.
name: Saracco, Fabio
name: Squartini, Tiziano
name: Shutters, Shade T.
name: Ulrich, Werner
name: Wang, Guanyang
name: Strona, Giovanni
Publisher: name: arXiv
Year: 2023
Subjects: subject: Data Analysis, Statistics and Probability (physics.data-an)
subject: FOS: Physical sciences

description: Two dimensional matrices with binary (0/1) entries are a common data structure in many research fields. Examples include ecology, economics, mathematics, physics, psychometrics and others. Because the columns and rows of these matrices represent distinct entities, they can equivalently be expressed as a pair of bipartite networks that are linked by projection. A variety of diversity statistics and network metrics can then be used to quantify patterns in these matrices and networks. But what should these patterns be compared to? In all of these disciplines, researchers have recognized the necessity of comparing an empirical matrix to a benchmark set of "null" matrices created by randomizing certain elements of the original data. This common need has nevertheless promoted the independent development of methodologies by researchers who come from different backgrounds and use different terminology. Here, we provide a multidisciplinary review of randomization techniques for matrices representing binary, bipartite networks. We aim to translate the concepts from different technical domains into a common language that is accessible to a broad scientific audience. Specifically, after briefly reviewing examples of binary matrix structures across different fields, we introduce the major approaches and common strategies for randomizing these matrices. We then explore the details of and performance of specific techniques, and discuss their limitations and computational challenges. In particular, we focus on the conceptual importance and implementation of structural constraints on the randomization, such as preserving row or columns sums of the original matrix in each of the randomized matrices. Our review serves both as a guide for empiricists in different disciplines, as well as a reference point for researchers working on theoretical and methodological developments in matrix randomization methods.
Additional file 1: of Frequency of EGFR T790M mutation and multimutational profiles of rebiopsy samples from non-small cell lung cancer developing acquired resistance to EGFR tyrosine kinase inhibitors in Japanese patients
Creators: name: Ko, Ryo
name: Kenmotsu, Hirotsugu
name: Masakuni Serizawa
name: Koh, Yasuhiro
name: Wakuda, Kazushige
name: Ono, Akira
name: Tetsuhiko Taira
name: Tateaki Naito
name: Haruyasu Murakami
name: Isaka, Mitsuhiro
name: Endo, Masahiro
name: Nakajima, Takashi
name: Ohde, Yasuhisa
name: Yamamoto, Nobuyuki
name: Takahashi, Kazuhisa
name: Takahashi, Toshiaki
Publisher: name: Figshare
Year: 2016
Subjects: subject: Space Science
subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Molecular Biology
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Cancer
subject: Hematology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Plant Biology
subject: 60506 Virology
subject: Computational Biology

description: The detail of mutational analysis. (DOCX 22 kb)
Additional file 1: Figure S1. of Role of IL-33 and ST2 signalling pathway in multiple sclerosis: expression by oligodendrocytes and inhibition of myelination in central nervous system
Creators: name: Allan, Debbie
name: Fairlie-Clarke, Karen
name: Elliott, Christina
name: Schuh, Cornelia
name: Barnett, Susan
name: Lassmann, Hans
name: Linnington, Christopher
name: Jiang, Hui-Rong
Publisher: name: Figshare
Year: 2016
Subjects: subject: Biochemistry
subject: Space Science
subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Physiology
subject: Immunology
subject: FOS: Clinical medicine
subject: Developmental Biology
subject: Cancer
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: 60506 Virology

description: Immunohistochemical staining of IL-33 and ST2 in human lung tissues. (A) IL-33 matched isotype control antibody staining in human lung (a) and brain (b) samples, and IL-33 staining in human lung sample (c and d). (B) ST2 matched isotype control antibody staining in human lung (a) and brain (b) tissues; ST2 staining in human lung sample (c and d). (a, b and c), x10 magnification; d. x25 magnification. (PDF 215 kb)
Universal Dynamics at the Lowest Temperatures
Creators: name: Siovitz, Ido
name: Heinen, Philipp
name: Rasch, Niklas
name: Lannig, Stefan
name: Deller, Yannick
name: Strobel, Helmut
name: Oberthaler, Markus
name: Gasenzer, Thomas
Publisher: name: arXiv
Year: 2023
Subjects: subject: Quantum Gases (cond-mat.quant-gas)
subject: High Energy Physics - Lattice (hep-lat)
subject: Pattern Formation and Solitons (nlin.PS)
subject: FOS: Physical sciences
subject: G.3; I.6.8

description: High-performance graphical processing units (GPU) are used for the repeated parallelised propagation of non-linear partial differential equations on large spatio-temporal grids. The main challenge results as a combination of the requirement of large grids for exploring scaling over several orders of magnitude, both in space and time, and the need for high statistics in averaging over many runs, in computing correlation functions for highly fluctuating quantum many-body states. With our simulations, we explore the dynamics of complex quantum systems far from equilibrium, with the aim of classifying their universal characteristics such as scaling exponents near non-thermal fixed points. Our results are strongly relevant for the development of synthetic quantum systems when exploring the respective physics in the laboratory.
description: 6 pages, 2 figures, Proceedings of the 8th bwHPC-Symposium, organized by the High-Performance Computing Center Stuttgart (HLRS) (2022)
Additional file 3: Figure S3. of Role of IL-33 and ST2 signalling pathway in multiple sclerosis: expression by oligodendrocytes and inhibition of myelination in central nervous system
Creators: name: Allan, Debbie
name: Fairlie-Clarke, Karen
name: Elliott, Christina
name: Schuh, Cornelia
name: Barnett, Susan
name: Lassmann, Hans
name: Linnington, Christopher
name: Jiang, Hui-Rong
Publisher: name: Figshare
Year: 2016
Subjects: subject: Microbiology
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Neuroscience
subject: Immunology
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Science Policy

description: The number of axons and myelinated axons at DIV 12, 18 and 28 of the rat CNS myelinating culture. (A) Percentage of SMI-31+ cells in view field; (B) Percentage of MBP+ axons in view filed. (C) Representative images of SMI-31 and MBP staining in the myelinating culture at DIV 12, 18 and 28. Data are presented as Mean + SEM, and were compiled from three independent experiments. (DOC 356 kb)
Monoecocestus undefined-2
Creators: name: Martins, Natalia Beatriz Guerreiro
name: Robles, María Del Rosario
name: Navone, Graciela Teresa
name: Callejón, Rocío
Publisher: name: Zenodo
Year: 2023
Subjects: Biodiversity
Taxonomy
Animalia
Platyhelminthes
Cestoda
Cyclophyllidea
Anoplocephalidae
Monoecocestus
Monoecocestus undefined-2

description: Monoecocestus sp.2
Description (based on three specimens): Scolex 0.27 long by 0.41 wide (Fig. 1g). Suckers 0.16 ± 0.01 (0. 17–0. 26) by 0.13 ± 0.01 (0.12–0.14) in diameter. Mature proglottids 0.72 ± 0.32 (0.49–0.94) long by 2.60 ± 0.23 (2.43–2.76) wide (Fig. 1h). Genital pores alternate irregularly. Testes number 90 per proglottid, each testis 0,04 ± 0.01 (0.03– 0.05) in diameter. Cirrus sac 0.13 long by 0.36 wide. Vitellarium 0.42 ± 0.25 (0.27–0.71) wide. Ovary 0.63 ± 0.28 (0.32–0.87) wide. Gravid proglottids 1.18 ± 0.01 (1.17–1.18) long by 2.54 ± 0.01 (2.53–2.55) wide. Eggs 43.04 ± 0.09 (42.97–43.10) μm long by 39.10 ± 0.18 (38.97–39.22) μm wide (Fig. 1i). Embryophore in form of a pyriform apparatus.
Taxonomic summary
Host: Holochilus chacarius
Locality: Selvas de Río de Oro, Chaco Province
Voucher specimens: MLP-He 7588
Comments. These specimens were classified under the genus Monoecocestus following Beveridge (1994), based on its morphological features, e.g., simple genitalia, genital pores irregularly alternate, internal and external seminal vesicles present, pyriform apparatus present. However, due to inadequate preservation, morphological characteristics of the uterus could not be well observed. Among species with genital pores irregularly alternate, Monoecocestus sp.2 differ from M. eljefe, M. diplomys, M. machadoi, M. minor, M. myopotami, and M. sininterus, by testes number; from M. mackiewiczi, and M. microcephalus by size of scolex and suckers; and from M. andersoni by size of mature proglottids, testes and eggs. In addition, Monoecocestus sp.2 differ from Monoecocestus sp.1 by size of scolex (0.27 x 0.41 vs. 0.11 x 0.14), mature and gravid proglottids (0.72 x 2.60 vs. 0.51 x 1.70; 1.18 x 2.54 vs. 1.17 x 1.85, respectively), testes number (90 vs. 45), and diameter of eggs (43.04 x 39.22 μm vs. 45.5 x 42.8 μm).
description: Published as part of Martins, Natalia Beatriz Guerreiro, Robles, María Del Rosario, Navone, Graciela Teresa & Callejón, Rocío, 2023, Monoecocestus (Cestoda: Anoplocephalidae) diversity in Sigmodontinae rodents characterized by morphology and molecular methods, pp. 37-55 in Zootaxa 5380 (1) on page 46, DOI: 10.11646/zootaxa.5380.1.3, http://zenodo.org/record/10212862
Polypedilum asoprimum Bidawid & Fittkau 1995
Creators: name: Zhang, Ruilei
name: Song, Chao
name: Qi, Xin
name: Wang, Xinhua
Publisher: name: Zenodo
Year: 2016
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Diptera
Chironomidae
Polypedilum
Polypedilum asoprimum

description: asoprimum Sasa & Suzuki, 1991: Research Report from Toyama Prefectural Environmental Pollution Research Center, 1991: 94 (Polypedilum).
= togaexpansum Sasa & Okazawa, 1991, Research Report from Toyama Prefectural Environmental Pollution Research Center, 1991: 109 (Polypedilum).
Type locality. Japan, Jigoku-onsen, Aso National Park, Kumamoto Prefecture.
Distribution. PA: Japan, Russian Far East.
description: Published as part of Zhang, Ruilei, Song, Chao, Qi, Xin & Wang, Xinhua, 2016, Taxonomic review on the subgenus Tripodura Townes (Diptera: Chironomidae: Polypedilum) from China with eleven new species and a supplementary world checklist, pp. 1-53 in Zootaxa 4136 (1) on page 41, DOI: 10.11646/zootaxa.4136.1.1, http://zenodo.org/record/399782
Mathematical analysis of modified level-set equations
Creators: name: Bothe, Dieter
name: Fricke, Mathis
name: Soga, Kohei
Publisher: name: arXiv
Year: 2023
Subjects: subject: Analysis of PDEs (math.AP)
subject: FOS: Mathematics

description: The linear transport equation allows to advect level-set functions to represent moving sharp interfaces in multiphase flows as zero level-sets. A recent development in computational fluid dynamics is to modify the linear transport equation by introducing a nonlinear term to preserve certain geometrical features of the level-set function, where the zero level-set must stay invariant under the modification. The present work establishes mathematical justification for a specific class of modified level-set equations on a bounded domain, generated by a given smooth velocity field in the framework of the initial/boundary value problem of Hamilton-Jacobi equations. The first main result is the existence of smooth solutions defined in a time-global tubular neighborhood of the zero level-set, where an infinite iteration of the method of characteristics within a fixed small time interval is demonstrated; the smooth solution is shown to possess the desired geometrical feature. The second main result is the existence of time-global viscosity solutions defined in the whole domain, where standard Perron's method and the comparison principle are exploited. In the first and second main results, the zero level-set is shown to be identical with the original one. The third main result is that the viscosity solution coincides with the local-in-space smooth solution in a time-global tubular neighborhood of the zero level-set, where a new aspect of localized doubling the number of variables is utilized.
Engineering Phonon-Qubit Interactions using Phononic Crystals
Creators: name: Kuruma, Kazuhiro
name: Pingault, Benjamin
name: Chia, Cleaven
name: Haas, Michael
name: Joe, Graham D
name: Assumpcao, Daniel Rimoli
name: Ding, Sophie Weiyi
name: Jin, Chang
name: Xin, C. J.
name: Yeh, Matthew
name: Sinclair, Neil
name: Lončar, Marko
Publisher: name: arXiv
Year: 2023
Subjects: subject: Quantum Physics (quant-ph)
subject: Optics (physics.optics)
subject: FOS: Physical sciences

description: The ability to control phonons in solids is key for diverse quantum applications, ranging from quantum information processing to sensing. Often, phonons are sources of noise and decoherence, since they can interact with a variety of solid-state quantum systems. To mitigate this, quantum systems typically operate at milli-Kelvin temperatures to reduce the number of thermal phonons. Here we demonstrate an alternative approach that relies on engineering phononic density of states, drawing inspiration from photonic bandgap structures that have been used to control the spontaneous emission of quantum emitters. We design and fabricate diamond phononic crystals with a complete phononic bandgap spanning 50 - 70 gigahertz, tailored to suppress interactions of a single silicon-vacancy color center with resonant phonons of the thermal bath. At 4 Kelvin, we demonstrate a reduction of the phonon-induced orbital relaxation rate of the color center by a factor of 18 compared to bulk. Furthermore, we show that the phononic bandgap can efficiently suppress phonon-color center interactions up to 20 Kelvin. In addition to enabling operation of quantum memories at higher temperatures, the ability to engineer qubit-phonon interactions may enable new functionalities for quantum science and technology, where phonons are used as carriers of quantum information.
Additional file 3: Figure S1. of Transcriptome analysis in calorie-restricted rats implicates epigenetic and post-translational mechanisms in neuroprotection and aging
Creators: name: Wood, Shona
name: Sipko Dam
name: Craig, Thomas
name: Tacutu, Robi
name: OâToole, Amy
name: Merry, Brian
name: JoĂŁo De MagalhĂŁes
Publisher: name: Figshare
Year: 2015
Subjects: subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: Developmental Biology

description: Enriched GO terms as a network generated from genes differentially expressed between AL and CR. (PDF 64 kb)
Monoecocestus undefined-3
Creators: name: Martins, Natalia Beatriz Guerreiro
name: Robles, María Del Rosario
name: Navone, Graciela Teresa
name: Callejón, Rocío
Publisher: name: Zenodo
Year: 2023
Subjects: Biodiversity
Taxonomy
Animalia
Platyhelminthes
Cestoda
Cyclophyllidea
Anoplocephalidae
Monoecocestus
Monoecocestus undefined-3

description: Monoecocestus sp.3
Description (based on two specimens): strobila total length 2.11; 3.05. Number of proglottids 20; 22 (Fig. 2g). Scolex 0.25 long by 0.32 wide (Fig. 1j). Suckers 0.13–0.15 in diameter. Mature proglottids 0.10–0.15 long by 0.55–0.77 wide (Fig. 1k). Genital pores alternate regularly. Testes number 50–56 per proglottid, overlap ovary and vitelline gland. Cirrus sac 0.20 long by 0.08 wide, extended to midline of proglottid. Cirrus with spines (Fig. 2h). Ovary 0.25 wide. Vitellarium 0.06 wide. Gravid proglottids 0.30–0.44 long by 0.40–0.48 wide. Eggs 40.55 ± 5.64 (35.6–46.42) μm in diameter (Fig. 1l). Embryophore in form of a pyriform apparatus.
Taxonomic summary
Host: Akodon azarae
Locality: Balcarce, Buenos Aires Province
Voucher specimens: MLP-He 840
Comments. These specimens were classified under the genus Monoecocestus following Beveridge (1994), based on its morphological features, e.g., genitalia single, genital pore regularly alternate, uterus reticulated, pyriform apparatus present. Among species with genital pores regularly alternate, Monoecocestus sp.3 is separated from Monoecocestus americanus (Stiles, 1895), Monoecocestus anoplocephaloides (Douthitt, 1915), Monoecocestus centroovarium Dronen, Pitts & Smolen, 1994, Monoecocestus erethizonthis Beddard 1914, Monoecocestus giganticus Buhler, 1970, Monoecocestus gundlachi Vigueras, 1943, Monoecocestus hagmanni (Janicki, 1904), M. hydrochoeri, Monoecocestus jacobi Sinkoc, Müller & Brum, 1998, M. machadoi, Monoecocestus macrobursatum Rêgo, 1961, Monoecocestus parcitesticulatus Rêgo, 1960, Monoecocestus petiso Haverkost & Gardner, 2010, Monoecocestus sigmodontis (Chandler & Suttles, 1922), Monoecocestus thomasi Rausch & Masert, 1977, M. threlkeldi, and Monoecocestus torresi Olsen, 1976 by testes number; from Monoecocestus variabilis (Douthitt, 1915) by strobila length, size of scolex and suckers; and from Monoecocestus poralus Haverkost & Gardner, 2010 by strobila length, size mature proglottids, cirrus sac and eggs.
description: Published as part of Martins, Natalia Beatriz Guerreiro, Robles, María Del Rosario, Navone, Graciela Teresa & Callejón, Rocío, 2023, Monoecocestus (Cestoda: Anoplocephalidae) diversity in Sigmodontinae rodents characterized by morphology and molecular methods, pp. 37-55 in Zootaxa 5380 (1) on pages 46-47, DOI: 10.11646/zootaxa.5380.1.3, http://zenodo.org/record/10212862
A mono-atomic orbital-based 1D topological crystalline insulator
Creators: name: Liu, Gengming
name: Workman, Violet
name: Noh, Jiho
name: Ma, Yuhao
name: Hughes, Taylor L.
name: Benalcazar, Wladimir A.
name: Bahl, Gaurav
Publisher: name: arXiv
Year: 2023
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: Topological crystalline insulators (TCIs) are classified by topological invariants defined with respect to the crystalline symmetries of their gapped bulk. The bulk-boundary correspondence then links the topological properties of the bulk to robust observables on the edges, e.g., the existence of robust edge modes or fractional charge. In one dimension, TCIs protected by reflection symmetry have been realized in a variety of systems where each unit cell has spatially distributed degrees of freedom (SDoF). However, these realizations of TCIs face practical challenges stemming from the sensitivity of the resulting edge modes to variations in edge termination and to the local breaking of the protective spatial symmetries by inhomogeneity. Here we demonstrate topologically protected edge states in a mono-atomic, orbital-based TCI that mitigates both of these issues. By collapsing all SDoF within the unit cell to a singular point in space, we eliminate the ambiguity in unit cell definition and hence remove a prominent source of boundary termination variability. The topological observables are also more tolerant to disorder in the orbital energies. To validate this concept, we experimentally realize a lattice of mechanical resonators where each resonator acts as an "atom" that harbors two key orbital degrees of freedom having opposite reflection parity. Our measurements of this system provide direct visualization of the $sp$-hybridization between orbital modes that leads to a non-trivial band inversion in the bulk. Furthermore, as the spatial width of the resonators is tuned, one can drive a transition between a topological and trivial phase. In the future we expect our approach can be extended to realize orbital-based obstructed atomic insulators and TCIs in higher dimensions.
Rohling et al P&P: R-codes with input and output files.
Creators: name: Rohling, Eelco
Publisher: name: figshare
Year: 2024
Subjects: classificationCode: 370904
subject: Palaeoclimatology

description: There are two R-code files (each uses the same three input .txt files that are given also).These are for the Revised main run with original clumped isotope data as originally published by Meckler et al. (2022), and for an additional run with lowered clumped isotope temperatures after Daeron and Gray (2023). In both scripts, the ice-sheet aspect ratio (eps) is set in Line 36 to 2x10^-3, for steep ice sheets. For the flat ice-sheet experiments, we halved this to 1x10^-3.Also included is a 4-sheet excel file with key model outputs, named Rohling et al -REVISED_Outputs.xlsx. The sheet-names on the tabs indicate for which experiments these selected output values are given. Values are changes relative to present. Note that sea level change relative to the present is given by -1 x (Volume_all).
Additional file 2: Figure S2. of Role of IL-33 and ST2 signalling pathway in multiple sclerosis: expression by oligodendrocytes and inhibition of myelination in central nervous system
Creators: name: Allan, Debbie
name: Fairlie-Clarke, Karen
name: Elliott, Christina
name: Schuh, Cornelia
name: Barnett, Susan
name: Lassmann, Hans
name: Linnington, Christopher
name: Jiang, Hui-Rong
Publisher: name: Figshare
Year: 2016
Subjects: subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Neuroscience
subject: Immunology
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Science Policy

description: The number of oligodendrocytes in the rat CNS myelinating co-cultures. (A) Percentage of Olig2+ cells in total field. (B) Images of Olig2 staining in the culture system at DIV 12, 18 and 28. Data are presented as Mean + SEM, and were compiled from three independent experiments. (PDF 189 kb)
Polypedilum asurini Bidawid-Kafka 1996
Creators: name: Zhang, Ruilei
name: Song, Chao
name: Qi, Xin
name: Wang, Xinhua
Publisher: name: Zenodo
Year: 2016
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Diptera
Chironomidae
Polypedilum
Polypedilum asurini

description: asurini Bidawid-Kafka, 1996: Entomofauna, 17: 184 (Polypedilum (Tripodura )).
Type locality. Brazil (Oberlauf des Rio Paru de Oeste, Mission Tirio).
Distribution. NT: Brazil (Pará, Amazonas).
description: Published as part of Zhang, Ruilei, Song, Chao, Qi, Xin & Wang, Xinhua, 2016, Taxonomic review on the subgenus Tripodura Townes (Diptera: Chironomidae: Polypedilum) from China with eleven new species and a supplementary world checklist, pp. 1-53 in Zootaxa 4136 (1) on page 41, DOI: 10.11646/zootaxa.4136.1.1, http://zenodo.org/record/399782