cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Miconia pusilliflora Naudin 1850
Creators: name: Silva-Gonçalves, Kelly Cristina Da
name: Baumgratz, José Fernando A.
name: Nunes-Freitas, André Felippe
Publisher: name: Zenodo
Year: 2014
Subjects: Biodiversity
Taxonomy
Plantae
Tracheophyta
Magnoliopsida
Myrtales
Melastomataceae
Miconia
Miconia pusilliflora

description: 5.10. Miconia pusilliflora (Candolle 1828: 194) Naudin (1850: 171). [Figs. 3o, 8j–m]
 Trees 7–13 m; indumentum of the branches, leaves, inflorescences, hypanthium and calyx furfuraceous-stellulate, trichomes early-caducous. Petioles 1.5–2.4 cm long; blade 8.6–25 × 1.9–5.3 cm, green subconcolour, chartaceous, elliptic, base acute, apex acuminate to caudate, margin serrulate; acrodromous basal veins 3; domatia absent. Thyrsoids 3.6–11.5 cm long, no branchlets of glomerules; bracts caducous, not seen; bracteoles 0.3–0.9 × 0.1–0.2 mm, lineartriangular, caducous. Flowers 4–5-merous, pedicelate; hypanthium 0.9–1.1 × 0.9–1 mm, campanulate; inner torus glabrous; calyx caducous, lobes 0.9–1 × 0.8–0.9 mm, triangular, margin ciliolate; petals 1.1–1.5 × 0.9–1 mm, white, asymmetric, apex rounded; stamens isomorphic, equal in size, filaments 1.8–2 mm long; anthers 1.3–1.5 mm long, white, straight, pore ventral, very wide and prolonged to the base as a longitudinal slit, connective ca. 0.2 mm prolonged, unappendaged; ovary 0.2–0.3 × 0.4–0.5 mm, inferior, 3-celled, glabrescent; style 3-3.2 mm long, glabrous. Baccaceous 2–4 × 1.3–3.5 mm, costate when young, oligospermous (2–6 seeds); seeds 2.8–3.8 × 1.8–2 mm, ovate to suborbicular, convex, testa smooth, slightly sulcate along the length.
 Specimens examined:— 2.III.2008, fl., R.S. Nunes 2 (RBR); 27.IX.2009, fr., K.C. Silva 58 (RBR); 19.III.2010, fl., K.C. Silva 81 (RBR); 15.V.2010, fl., fr., K.C. Silva & F.S. Gonçalves 101 (RBR).
 Distribution:— Miconia pusilliflora occurs in Brazil, Argentina and Paraguay. In Brazil it is endemic to the Atlantic Forest Biome, and found from the state of Bahia to Rio Grande do Sul (Goldenberg 2009, 2012).
 Comments:—This is the first record to Marambaia, where this species occurs in Restinga Forest and Dense Submontane Ombrophilous Forest. It can also be distinguished by the green subconcolored leaves, with acuminate to caudate apices, serrulate margins, and the young costate fruits. A peculiar morphological characteristic is the presence of domatia on the abaxial leaf surface, but those may be absent (Baumgratz 1984, Baumgratz et al. 2006, Goldenberg 2009). In specimens of M. pusilliflora from Marambaia, these foliar structures have not been found. Additional illustrations in Cogniaux (1883 –1888), and Baumgratz et al. (2006).
description: Published as part of Silva-Gonçalves, Kelly Cristina Da, Baumgratz, José Fernando A. & Nunes-Freitas, André Felippe, 2014, Melastomataceae in a continental Atlantic Forest island from southeastern Brazil, pp. 61-92 in Phytotaxa 183 (2) on page 79, DOI: 10.11646/phytotaxa.183.2.1, http://zenodo.org/record/5149548
Magnetically Arrested Disk: An Energetically Efficient Accretion Flow
Creators: name: Narayan, Ramesh
name: Igumenshchev, Igor V.
name: Abramowicz, Marek A.
Publisher: name: arXiv
Year: 2003
Subjects: subject: Astrophysics (astro-ph)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: We consider an accretion flow model originally proposed by Bisnovatyi-Kogan & Ruzmaikin (1974), which has been confirmed in recent 3D MHD simulations. In the model, the accreting gas drags in a strong poloidal magnetic field to the center such that the accumulated field disrupts the axisymmetric accretion flow at a relatively large radius. Inside the disruption radius, the gas accretes as discrete blobs or streams with a velocity much less than the free-fall velocity. Almost the entire rest mass energy of the gas is released as heat, radiation and mechanical/magnetic energy. Even for a non-rotating black hole, the efficiency of converting mass to energy is of order 50% or higher. The model is thus a practical analog of an idealized engine proposed by Geroch and Bekenstein.
description: 4 pages, 2 figure, new refs added, in print in PASJ
Analysis of the National Health Service Institute for Innovation and Improvement Sustainability Model: A Scoping Review Protocol
Creators: name: Bert, Laetitia
name: Aldanie Rho
name: Bergeron, Frédéric
name: Côté-Boileau, Elizabeth
name: Jean-Louis Denis
name: Maher, Lynne
name: Archambault, Patrick Michel
Publisher: name: figshare
Year: 2021
Subjects: subject: 111709 Health Care Administration
subject: FOS: Health sciences
subject: 111708 Health and Community Services
subject: 111799 Public Health and Health Services not elsewhere classified

description: This is a scoping review protocol based on Levac’s (2010) six-stage scoping review methodology. The study will present a systematic synthesis of the evidence supporting the use of the NHS Sustainability Model for decision makers planning the implementation of healthcare innovations and identify knowledge gaps for future research concerning the NHS SM.
A parameterized catalog of radio galaxies as ultra-high energy cosmic ray sources
Creators: name: Rachen, Jörg P.
name: Eichmann, Björn
Publisher: name: arXiv
Year: 2019
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: Many attempts have been made to provide catalogs of potential sources of ultra-high energy cosmic ray (UHECR) particles based on various astronomical tracers, such as observed radio or gamma-ray emission. A closer look reveals, however, that they all suffer from significant bias and selection effects. We present here a demo-version of a catalog for one often-discussed UHECR source class, radio galaxies (or radio-loud AGN), which is based on a complete theoretical description of jet-energetics, particle acceleration physics, relativistic beaming effects and nuclear composition, parametrized by a comprehensible set of adjustable physical quantities. In addition to the bright radio galaxies Centaurus A, Virgo A, Fornax A and Cygnus A discussed in previous work, we find several sources with blazar-like properties that can contribute on a similar level if relativistic beaming effects are considered. We present a simple method to test the basic properties of the catalog for any choice of parameters (without the need to run expensive simulations), and find that in the canonical case the anisotropy signals expected from radio galaxies promise to be in good agreement with current observational findings. In particular, radio galaxies can reproduce almost exactly the direction of the dipole above 8 EeV detected by the Pierre Auger Observatory if we assume that extragalactic magnetic fields are strong (>1nG) only in structures, but very weak in voids. We plan to provide a completed and improved version of this catalog in electronic form, to be used in more detailed UHECR propagation simulations. For immediate applications, we suggest a complete set of 16 strong UHECR sources which can contribute to UHECR anisotropy on the level which can be currently probed by experiment, and note that 6 of them have not been considered in any previous studies.
description: 8 pages, 2 figures, paper presented at the 36th International Cosmic Ray Conference (ICRC2019), July 24th - August 1st, Madison, WI, USA; updated and final version
An Altmetric Analysis of Top Journals in Library and Information Science
Creators: name: Rangaswamy
name: H, Dr.Rajendra Babu
Publisher: name: figshare
Year: 2020
Subjects: subject: Library and Information Studies
subject: FOS: Media and communications

description: The current research examines that, which journals and article will get high citations as well as altmetrics attention score in the field of Library and Information Science. Purpose of this study analysed to 5 LIS journals indexed by Google Scholar Metrics 2019. The study results reveal that JAIS&T journal got 1st position with h5-Index. In this study significantly found that mostly used altmetrics source in LIS research was Mendeley (1998), followed by Twitter (113) and Blog (6) respectively. The highest altmetrics presence was seen in this study “Bibliometrix: An R-tool for Comprehensive Science Mapping Analysis” article with (50)Altmetrics Attention Score.
Ingerophrynus celebensis
Creators: name: Figueroa, Alex
name: Low, Martyn E. Y.
name: Lim, Kelvin K. P.
Publisher: name: Zenodo
Year: 2023
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Amphibia
Anura
Bufonidae
Ingerophrynus
Ingerophrynus celebensis

description: Ingerophrynus celebensis (Ģnther, 1859) — Erroneous.
Celebes Toad
Singapore records.
No published records.
Remarks. As I. celebensis is endemic to Sulawesi (Kurniati & Laksono 2021), the locality of Singapore for NMW-5435 is clearly an error. The specimens were donated to NMW by Steindachner in 1866 and were likely traded in Singapore.
LKCNHM & NHMUK Museum specimens. No specimens.
Additional Singapore museum specimens. Singapore (no locality): NMW.
description: Published as part of Figueroa, Alex, Low, Martyn E. Y. & Lim, Kelvin K. P., 2023, Singapore's herpetofauna: updated and annotated checklist, history, conservation, and distribution, pp. 1-378 in Zootaxa 5287 (1) on page 256, DOI: 10.11646/zootaxa.5287.1.1, http://zenodo.org/record/7960319
Keep the term « heavy metal »​ for music not for science! Let’s continue to educate!
Creators: name: Pourret, Olivier
Publisher: name: figshare
Year: 2020
Subjects: subject: 50204 Environmental Impact Assessment
subject: FOS: Earth and related environmental sciences

description: Blog article https://olivierpourret.wordpress.com/
Shallow Deep Transitions of Neutral and Charged Donor States in Semiconductor Quantum Dots
Creators: name: Pandey, R. K.
name: Harbola, Manoj K.
name: Singh, Vijay A.
Publisher: name: arXiv
Year: 2003
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: We carry out a detailed investigation of neutral ($D^0$) and charged ($D^-$) impurity states of hydrogen-like donors in spherical semiconductor quantum dots. The investigation is carried out within the effective mass theory (EMT). We take recourse to local density approximation (LDA) and the Harbola-Sahni (HS) schemes for treating many-body effects. We experiment with a variety of confining potentials: square, harmonic and triangular. We observe that the donor level undergoes shallow to deep transition as the dot radius ($R$) is reduced. On further reduction of the dot radius it becomes shallow again. We term this non-monotonic behaviour \textbf{SHADES}. This suggests the possibility of carrier {\textbf{\textit{``freeze out''}}} for both $D^0$ and $D^-$. Further, our study of the optical gaps also reveals a {\textbf{SHADES}} transition.
description: 19 pages, 8 figures, Revised Version
Motion control for autonomous heterogeneous multi-agent area search in uncertain conditions
Creators: name: Ivić, Stefan
Publisher: name: arXiv
Year: 2019
Subjects: subject: Optimization and Control (math.OC)
subject: Multiagent Systems (cs.MA)
subject: Robotics (cs.RO)
subject: FOS: Mathematics
subject: FOS: Computer and information sciences

description: Using multiple mobile robots in search missions offers a lot of benefits, but one needs a suitable and competent motion control algorithm which is able to consider sensors characteristics, the uncertainty of target detection and complexity of needed maneuvers in order to make a multi-agent search autonomous. This paper provides a methodology for an autonomous two-dimensional search using multiple unmanned search agents. The proposed methodology relies on an accurate calculation of target occurrence probability distribution based on the initial estimated target distribution and continuous action of spatial variant search agent sensors. The core of the autonomous search process is a high-level motion control for multiple search agents which utilizes the probabilistic model of target occurrence via Heat Equation Driven Area Coverage (HEDAC) method. This centralized motion control algorithm is tailored for handling a group of search agents which are heterogeneous in both motion and sensing characteristics. The motion of agents is directed by the gradient of the potential field which provides near-ergodic exploration of the search space. The proposed method is tested on three realistic search mission simulations and compared with three alternative methods, where HEDAC outperforms all alternatives in all tests. Conventional search strategies need about double the time to achieve proportionate detection rate when compared to HEDAC controlled search. The scalability test showed that increasing the number of HEDAC controlled search agents, although somewhat deteriorating the search efficiency, provides needed speed-up of the search. This study shows the flexibility and competence of the proposed method and gives a strong foundation for possible real-world applications.
description: v1
Additional file 2 of Gasdermin E regulates the stability and activation of EGFR in human non-small cell lung cancer cells
Creators: name: Xu, Limei
name: Shi, Feifei
name: Wu, Yingdi
name: Yao, Shun
name: Wang, Yingying
name: Jiang, Xukai
name: Su, Ling
name: Liu, Xiangguo
Publisher: name: figshare
Year: 2023
Subjects: subject: Biochemistry
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Cancer
subject: Infectious Diseases
subject: FOS: Health sciences

description: Additional file 1. Figure S1. GSDME depletion suppresses the proliferation of NSCLC cells in vitro. Figure S2. The 3D structures of GSDME and EGFR. Figure S3. GSDME knockdown decreases protein levels of EGFR. Figure S4. Overexpression of GSDME (D270A) decreases phosphorylation of EGFRY1045. Figure S5. GSDME knockdown inhibited EGFR dimerization. Figure S6. Plasmid overexpression efficiency of GSDME-FL, GSDME-N and GSDME (D270A). Figure S7. An example figure of the flow cytometry gating strategy. Abbreviations of TCGA Cancers. KEY RESOURCES TABLE.
Existence of Bound States for Layers Built Over Hypersurfaces of Euclidean Space
Creators: name: Lin, Christopher
name: Lu, Zhiqin
Publisher: name: arXiv
Year: 2004
Subjects: subject: Differential Geometry (math.DG)
subject: Mathematical Physics (math-ph)
subject: FOS: Mathematics
subject: FOS: Physical sciences
subject: 58C40; 58E35

description: In this paper, we study the bound states of quantum layers. We prove that for the quantum layer built over a parabolic manifold which is not totally geodesic, if the second fundamantal form decays sufficiently fast, then the bound states exist. In the 2d case, we prove that the quantum layer over a convex surface whose second fundamental form tends to zero at infinity must have bound states.
description: 19 pages
Nierenschädigungen und der Einfluss von Tenofovir Disoproxilfumarat bei HIV-Patienten in Limbe, Kamerun
Creators: name: Rudolph, Jens Markus
Publisher: name: Universität Rostock
Year: 2019
Subjects: subject: 610 Medical sciences Medicine

description: Eine regelmäßige Überprüfung der Nierenfunktion bei HIV-Patienten in Limbe ist indiziert. Einerseits ist eine hohe Prävalenz an HIV-asssoziierter Nephropathien wahrscheinlich. Andererseits ist Tenofovir Disoproxilfumarat, für welches in Studien ein nephrotoxischer Effekt belegt ist, das am häufigsten eingesetzte antiretrovirale Medikament in der HIV-Ambulanz des Rgional Hospital Limbe.
Organic matter in Seyfert2 nuclei : comparison with our Galactic center lines of sight
Creators: name: Dartois, E.
name: Marco, O.
name: Muñoz-Caro, G. M.
name: Brooks, K.
name: Deboffle, D.
name: d'Hendecourt, L.
Publisher: name: arXiv
Year: 2004
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: We present ESO - Very Large Telescope and ESA - Infrared Space Observatory 3 to 4 $μ$m spectra of Seyfert 2 nuclei as compared to our galactic center lines of sight. The diffuse interstellar medium probed in both environments displays the characteristic 3.4 $μ$m aliphatic CH stretch absorptions of refractory carbonaceous material. The profile of this absorption feature is similar in all sources, indicating the CH$_2$/CH$_3$ ratios of the carbon chains present in the refractory components of the grains are the same in Seyfert 2 inner regions. At longer wavelengths the circumstellar contamination of most of the galactic lines of sight precludes the identification of other absorption bands arising from the groups constitutive of the aliphatics seen at 3.4 $μ$m. The clearer continuum produced by the Seyfert 2 nuclei represents promising lines of sight to constrain the existence or absence of strongly infrared active chemical groups such as the carbonyl one, important to understand the role of oxygen insertion in interstellar grains. The Spitzer Space Telescope spectrometer will soon allow one to investigate the importance of aliphatics on a much larger extragalactic sample.
description: 10 pages. Accepted for publication on April 30th 2004 in Astronomy and Astrophysics
Additional file 1 of Regulatory role of Chitinase 3-like 1 gene in papillary thyroid carcinoma proved by integration analyses of single-cell sequencing with cohort and experimental validations
Creators: name: Zhang, Xiaojun
name: Peng, Wanwan
name: Fan, Jie
name: Luo, Ruihua
name: Liu, Shanting
name: Du, Wei
name: Luo, Chaochao
name: Zheng, Jiawen
name: Pan, Xinghua
name: Ge, Hong
Publisher: name: figshare
Year: 2023
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Supplementary Material 1
Review of proton and nuclear shape fluctuations at high energy
Creators: name: Mäntysaari, Heikki
Publisher: name: arXiv
Year: 2020
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: High Energy Physics - Experiment (hep-ex)
subject: Nuclear Experiment (nucl-ex)
subject: Nuclear Theory (nucl-th)
subject: FOS: Physical sciences

description: Determining the inner structure of protons and nuclei in terms of their fundamental constituents has been one of the main tasks of high energy nuclear and particle physics experiments. This quest started as a mapping of the (average) parton densities as a function of longitudinal momentum fraction and resolution scale. Recently, the field has progressed to more differential imaging, where one important development is the description of the event-by-event quantum fluctuations in the wave function of the colliding hadron. In this Review, recent developments on the extraction of proton and nuclear transverse geometry with event-by-event fluctuations from collider experiments at high energy is presented. The importance of this fundamentally interesting physics in other collider experiments like in studies of the properties of the Quark Gluon Plasma is also illustrated.
description: 19 pages, 13 figures. Invited review published in Reports on Progress in Physics. v2: matches published version
Avoidance of teratogenic effects of ultraviolet radiation in a population of Boeckella poppei (Crustacea: Calanoida) from Livingston Island, Maritime Antarctica
Creators: name: Pandourski, Ivan
name: Evtimova, Vesela
name: Kenderov, Lyubomir
Publisher: name: Zenodo
Year: 2021
Subjects: Antarctica
Livingston Island
Boeckella poppei
pigmentation
offspring photoprotection

description: Antarctic environments are characterised with potentially high levels of ultraviolet radiation (UVR) damaging to living organisms. Aquatic organisms have different strategies to minimise their negative effects, e.g. behavioural (migrating to deeper aquatic layers) or biochemical (photoprotection or enzymatic repair of the incurred damages). The calanoid genus Boeckella has a high level of plasticity with regard to UVR, which ensures its wide distribution in different regions of Antarctica. Here we present a specific photoprotective reaction in the population of Boeckella poppei on the Livingston Island, Maritime Antarctica. In non-ovigerous females, we observed uniform distribution of carotenoids in the body, while these pigments were almost entirely concentrated in the oval sacs of mature females. We consider this a mechanism to protect the eggs from the teratogenic influence of the high level of UVR in Antarctic environments. Another mechanism for avoidance of the effects of UVR we observed was the migration of specimens of B. poppei towards the deeper zone of the Antarctic glacial lake Todorina buza. 5th Balkan Scientific Conference on Biology – Book of Abstracts, © Plovdiv University Press, 2021, eISBN 978-619-202-644-8
Ossaea marginata Triana 1871
Creators: name: Silva-Gonçalves, Kelly Cristina Da
name: Baumgratz, José Fernando A.
name: Nunes-Freitas, André Felippe
Publisher: name: Zenodo
Year: 2014
Subjects: Biodiversity
Taxonomy
Plantae
Tracheophyta
Magnoliopsida
Myrtales
Melastomataceae
Ossaea
Ossaea marginata

description: 6.1. Ossaea marginata (Desrousseaux 1797: 32) Triana (1871: 147). [Figs. 3p–q, 9a–c]
 Shrubs 1.3–1.7 m; indumentum of the branches, petioles, inflorescences, hypanthium and calyx furfuraceous-stellulate and setose. Petioles 1.6–4.4 cm long; blade 10.6–19 × 3.2–5.9 cm, papiraceous, elliptic, base obtuse, apex acuminate, margin entire or crenulate, appressed-ciliolate; adaxial surface densely appressed-setulose in the marginal region, abaxial surface also furfuraceous-stellulate; acrodromous veins 5, the inner pair 5–15 mm suprabasal. Botryoid and metabotryoid 0.9–16 mm long, axillary, in leafy and/or aphyllous nodes; bracts 0.8–1 × 0.1–0.2 mm, bracteoles 0.8– 0.9 × 0.1–0.2 mm, both persistent, triangular, apex acuminate. Floral buds with apex acute to acuminate. Flowers 5-merous, pedicelate; hypanthium ca. 3 × 2.1–3 mm, campanulate; inner torus setulose, glabrescent; calyx persistent, bilobed, external lobes 3.5–5 × 0.5–1 mm, narrowly triangular, margin densely ciliolate, internal lobes 0.7–0.8 × 1.8–2 mm, short-triangular to ovate; petals 3–3.2 × 1–1.1 mm, white, narrowly triangular, apex acute to acuminate; stamens equal in size and shape, filaments ca. 2 mm long; anthers ca. 2 mm long, yellow, straight, pore terminal, connective not prolonged bellow the thecae, appendage dorsal, obsolete; ovary ca. 1 × 1–2 mm, 3/4- inferior, 4- celled, sparsely setulose; style ca. 6 mm long, glabrous. Baccate, bacidium type, 5.5–8 × 4.5–7 mm, purple-blackness, sparsely furfuraceous-stellulate and setose, polyspermous; seeds 0.8–1 × 0.1–0.3 mm, obtriangular.
 Specimens examined:— 23.XII.2005, fl., fr., F.C. Nettesheim 162 (RBR); 12–13.X.2007, fl., fr., K.C. Silva 18 (RB, RBR); 12–13.X.2007, fr., K.C. Silva 19 (RB, RBR); 23.II.2008, fr., K.C. Silva 28 (RB, RBR); 9.I.2010, fr., K.C. Silva 62 (RBR).
 Distribution:—It occurs in Brazil, Argentina and Paraguay. In Brazil, it is found in the states of Mato Grosso do Sul, Minas Gerais, Espírito Santo, Rio de Jnaeiro, São Paulo, Paraná, and Santa Catarina, in Cerrado and Atlantic Forest Biomes (Souza & Baumgratz 2012b).
 Comments:—In Marambaia, this species occurs in Dense Sobmontane Ombrophuilous Forest. It can be distinguished by the axillary inflorescences at leafy and/or aphyllous nodes, the floral buds and petals with acute to acuminate apices, bilobed laciniate calyx, and the partly inferior ovary. Additional illustrations in Goldenberg et al. (2005), and Souza (2009).
description: Published as part of Silva-Gonçalves, Kelly Cristina Da, Baumgratz, José Fernando A. & Nunes-Freitas, André Felippe, 2014, Melastomataceae in a continental Atlantic Forest island from southeastern Brazil, pp. 61-92 in Phytotaxa 183 (2) on page 81, DOI: 10.11646/phytotaxa.183.2.1, http://zenodo.org/record/5149548
WORKSHOP: Online data analysis for biologists
Creators: name: Price, Gareth
name: Thang, Michael
Publisher: name: Zenodo
Year: 2024
Subjects: subject: Bioinformatics
subject: FOS: Computer and information sciences
subject: Data analysis
subject: Galaxy

description: This record includes training materials associated with the Australian BioCommons workshop ‘Online data analysis for biologists’. This workshop took place on 21 August 2024.

Topic description

Galaxy is a web-based platform that lets you conduct accessible, reproducible, and transparent computational biological research. Widely used by researchers world wide, Galaxy gives you access to 1000’s of popular tools for analysis and processing of biological data. It is perfect for working with a wide range of big and small datasets including genome assembly, annotation, epigenetics, metabolomics, metagenomics, proteomics, statistics, transcriptomics, variant analysis and visualisation.

This workshop provides an introduction to using Galaxy and available tools. Using an example dataset, you’ll practice uploading data, choosing and running tools, and viewing the results. We’ll share our top tips for managing your experiments and speeding up your analysis with workflows.

Lead trainer: Dr Gareth Price, Galaxy Australia

Facilitator: Mike Thang, Galaxy Australia / QCIF

Infrastructure provision: Galaxy Australia

Host: Dr Melissa Burke, Australian BioCommons

 

Training Materials

Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event.

Files and materials included in this record:

Event_metadata_Online_data_analysis_for_biologists_210824 (PDF): Information about the event logistics including, description, event URL, learning objectives, prerequisites, technical requirements etc.

Schedule_Online_data_analysis_for_biologists_210824 (PDF): Schedule for the workshop providing a breakdown of topics and timings

 

Materials shared elsewhere:

This workshop is based on the Galaxy Training Network tutorial ‘Galaxy basics for everyone’: https://training.galaxyproject.org/training-material/topics/introduction/tutorials/galaxy-intro-101-everyone/tutorial.html

A recording of this workshop is available on the Australian BioCommons YouTube Channel: https://www.youtube.com/watch?v=PF39KjOvreM
Theoretical and Phenomenological Aspects of CPT Violation
Creators: name: Mavromatos, Nick E.
Publisher: name: arXiv
Year: 2003
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: Astrophysics (astro-ph)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: I review briefly various models and ways of Quantum-Gravity induced CPT violation, and discuss in some detail their phenomenology, in particular precision CPT tests in neutral mesons, and hydrogen/antihydrogen spectroscopy. As I shall argue, severe constraints can be placed in CPT violating parameters, with sensitivities that can safely exclude models with effects suppressed by a single power of Planck mass.
description: 9 pages latex, Invited talk, LEAP03, Yokohama (Japan), 3-7 March 2003, Proc. Nucl. Instr. Methds. to appear
Exact NLO Matching and Analyticity in $b\to s\ell\ell$
Creators: name: Asatrian, Hrachia M.
name: Greub, Christoph
name: Virto, Javier
Publisher: name: arXiv
Year: 2019
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: High Energy Physics - Experiment (hep-ex)
subject: High Energy Physics - Lattice (hep-lat)
subject: FOS: Physical sciences

description: Exclusive rare decays mediated by $b\to s\ell\ell$ transitions receive contributions from four-quark operators that cannot be naively expressed in terms of local form factors. Instead, one needs to calculate a matrix element of a bilocal operator. In certain kinematic regions, this bilocal operator obeys some type of Operator Product Expansion, with coefficients that can be calculated in perturbation theory. We review the formalism and, focusing on the dominant SM operators ${\cal O}_{1,2}$, we perform an improved calculation of the NLO matching for the leading dimension-three operators. This calculation is performed completely analytically in the two relevant mass scales (charm-quark mass $m_c$ and dilepton squared mass $q^2$), and we pay particular attention to the analytic continuation in the complex $q^2$ plane. This allows for the first time to study the analytic structure of the non-local form factors at NLO, and to calculate the OPE coefficients far below $q^2=0$, say $q^2 \lesssim -10\,{\rm GeV}^2$. We also provide explicitly the contributions proportional to different charge factors, which obey separate dispersion relations.
description: 38 pages, 6 figures
Limnonectes kuhlii
Creators: name: Figueroa, Alex
name: Low, Martyn E. Y.
name: Lim, Kelvin K. P.
Publisher: name: Zenodo
Year: 2023
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Amphibia
Anura
Dicroglossidae
Limnonectes
Limnonectes kuhlii

description: Limnonectes kuhlii (Tschudi, 1838) — Erroneous.
Kuhl’s Fanged Frog
Singapore records.
Limnonectes kuhlii — Das & Haas, 2005: 380.
Remarks. Das & Haas (2005) cited Leong & Chou (1999) as a source for larval identification of L. kuhlii from Singapore. As L. kuhlii was not included in Leong & Chou (1999), and Das & Haas (2005) already included L. malesianus in their checklist, it’s most likely that they wrongly recognised L. blythii as L. kuhlii. Limnonectes kuhlii is a species complex composed of up to 22 cryptic lineages occurring throughout Asia that has since been broken up into numerous species (McLeod 2010), but no lineage ever existed in Singapore.
LKCNHM & NHMUK Museum specimens. No specimens.
Additional Singapore museum specimens. No specimens.
description: Published as part of Figueroa, Alex, Low, Martyn E. Y. & Lim, Kelvin K. P., 2023, Singapore's herpetofauna: updated and annotated checklist, history, conservation, and distribution, pp. 1-378 in Zootaxa 5287 (1) on page 257, DOI: 10.11646/zootaxa.5287.1.1, http://zenodo.org/record/7960319
Tibouchina Aublet 1775
Creators: name: Silva-Gonçalves, Kelly Cristina Da
name: Baumgratz, José Fernando A.
name: Nunes-Freitas, André Felippe
Publisher: name: Zenodo
Year: 2014
Subjects: Biodiversity
Taxonomy
Plantae
Tracheophyta
Magnoliopsida
Myrtales
Melastomataceae
Tibouchina

description: 7. Tibouchina Aublet (1775: 445).
 Trees or shrubs, sometimes treelets; branches flattened, terete or tetragonal, sometimes sharply or slightly winged. Inflorescences terminal; bracts and bracteoles persistent or caducous. Flowers 5-merous; calyx with lacinias unilobed, caducous; petals purple or lilac, obovate, apex asymmetric, margin ciliolate, glabrous; stamens purple to light purple, dimorphic and of two sizes, 5 larger antesepalous, 5 smaller antepetalous, anthers purple, lilac or pink, falciform or curve, pore terminal, connective prolonged bellow the thecae, appendage ventral, glabrous or pilose; ovary partly adnate to the hypanthium by septa along the length, free to the apex, 5-celled, pilose; stigma capitate. Capsule, velatidium or ruptidium type, polyspermous; seeds cochleate, granulate.
description: Published as part of Silva-Gonçalves, Kelly Cristina Da, Baumgratz, José Fernando A. & Nunes-Freitas, André Felippe, 2014, Melastomataceae in a continental Atlantic Forest island from southeastern Brazil, pp. 61-92 in Phytotaxa 183 (2) on page 81, DOI: 10.11646/phytotaxa.183.2.1, http://zenodo.org/record/5149548
Situating Improvisation: Exploring the Topology of Music and Hermeneutics
Creators: name: McAuliffe, Sam
Publisher: name: Monash University
Year: 2022
Subjects: subject: Philosophy
subject: FOS: Philosophy, ethics and religion

description: Improvisation is increasingly being recognised as central to a wide range of human activities. Yet despite its centrality, few have inquired into the underlying structure of improvisation as such. Beginning with improvisation in music, this thesis develops a hermeneutic-topological account of improvisation as an attending and responding to the situation in which one finds oneself. Working between music theory and philosophy, the thesis thereby advances an account of the structure of improvisation that is shown to be at work in musical performance but also in the conversational structure of understanding evident in the work of German philosopher, Hans-Georg Gadamer.
Mechanism Research of Regional Brand Enhancement Based on Agricultural Industry Clusters
Creators: name: Zhang, Yue-Li
name: Chen, Shu-Xia
name: Zhang, Yue-Li
name: Chen, Shu-Xia
Publisher: name: Unknown
Year: 2012
Subjects: subject: Agribusiness
subject: Agricultural industry clusters
subject: Regional brand
subject: Enhancement
subject: Mechanism

description: This article makes an integral and comprehensive study on the process of regional brand enhancement based on agricultural industry clusters using the theories of industrial clusters and regional brands. By analyzing the key determinants in the process of regional brand enhancement based on agricultural industry clusters, we establish a systemic theory system. The results show that as an important mediator in the process of regional brand enhancement based on agricultural industry clusters, the construction of value chain system is of vital importance. Other factors, such as the government guidance and service, the promotion of industry associations and professional cooperatives, play a key regulating role in this process.
Development of Urban Agriculture: A Case Study of Qianjin Village, Jiangxia District, Wuhan City
Creators: name: Guan, Bo
name: Shu, Chang-Jun
name: Guan, Bo
name: Shu, Chang-Jun
Publisher: name: Unknown
Year: 2012
Subjects: subject: Agribusiness
subject: Urban agriculture
subject: Development planning
subject: Qianjin Village

description: We take the case of Qianjin Village, Jiangxia District, Wuhan City, to research how to establish the system of urban agriculture with distinctive features relying on the advantage of urban resources. Under the guidance of guiding ideology, basic principles and overall objectives of urban agriculture development planning, we analyze the specific construction planning of urban agriculture in Qianjin Village, mainly including the construction of growing areas and construction of leisure areas. Then we put forth the security system of development of urban agriculture as follows: land transfer is the prerequisite of development of urban agriculture; policy support is the important foundation of development of urban agriculture; agricultural science and technology is strong support for development of urban agriculture; good leadership is the organizational guarantee for development of urban agriculture; the industrialization of agriculture is the main objective of development of urban agriculture.
Additional file 2 of Efficacy of a smartphone application for helping individuals with type 2 diabetes mellitus manage their blood glucose: a protocol for factorial design trial
Creators: name: Tang, Hongxia
name: Qin, Hua
name: Zhang, Mingjiao
name: Zhang, Jihong
name: Tan, Huiwen
name: Chen, Mengjie
name: Kong, Laixi
name: Guo, Maoting
name: Hu, Fenghui
name: Wang, Qin
name: Wang, Xiaoxia
name: Zhang, Kun
name: Xiong, Zhenzhen
Publisher: name: figshare
Year: 2023
Subjects: subject: Medicine
subject: Biotechnology
subject: Chemical Sciences not elsewhere classified
subject: Sociology
subject: FOS: Sociology
subject: Information Systems not elsewhere classified
subject: Science Policy
subject: Infectious Diseases
subject: FOS: Health sciences

description: Additional file 2.
Huh7 STR.pdf
Creators: name: Sun, Yuan
Publisher: name: figshare
Year: 2020
Subjects: subject: 111601 Cell Physiology
subject: FOS: Basic medicine

description: p.p1 {margin: 0.0px 0.0px 0.0px 0.0px; font: 12.0px Helvetica} Huh7 Cell Line Authentication Service STR Profile Report
Alleviating the Tension in the Cosmic Microwave Background using Planck-Scale Physics
Creators: name: Ashtekar, Abhay
name: Gupt, Brajesh
name: Jeong, Donghui
name: Sreenath, V.
Publisher: name: arXiv
Year: 2020
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: Certain anomalies in the CMB bring out a tension between the six-parameter flat $Λ$CDM model and the CMB data. We revisit the PLANCK analysis with loop quantum cosmology (LQC) predictions and show that LQC alleviates both the large-scale power anomaly and the tension in the lensing amplitude. These differences arise because, in LQC, the primordial power spectrum is scale dependent for small $k$, with a specific power suppression. We conclude with a prediction of larger optical depth and power suppression in the $B$-mode polarization power spectrum on large scales.
description: 6 pages, 5 figures, 1 table. The version that appeared in PRL. A few clarifications and several references added
Estimation and Dynamic Judgment of Urban-rural Coordinated Development: A Case Study of Chongqing City
Creators: name: Huang, Qing-Hua
name: Wang, Zhao
name: Jiang, Song
name: Liu, Jian-Hui
name: Huang, Qing-Hua
name: Wang, Zhao
name: Jiang, Song
name: Liu, Jian-Hui
Publisher: name: Unknown
Year: 2012
Subjects: subject: Agribusiness
subject: Urban-rural coordination degree
subject: AHP
subject: GCA
subject: GARCH
subject: Indicator system

description: Using AHP(Analytic Hierarchy Process) and GCA (Grey Comprehensive Analysis), this article measures the degree of urban-rural coordinated development of Chongqing City, and establishes GARCH model to analyze its dynamic feature. The results show that urban-rural coordination degree of Chongqing City tended to decline year by year in the period 1985-2010 on the whole; after it became a municipality directly under the Central Government, the average annual rate of decline reached 1.78%. Further, from GARCH modeling analysis, there is no "clustering" in urban-rural coordination degree of Chongqing City, and the impact of fluctuation state in the past on the future will gradually intensify. There is no "leverage effect" in urban-rural coordination degree of Chongqing City, and if the government does not exert "external force", urban-rural coordination degree will decline year by year. But in the long run, urban-rural coordination degree will gradually converge to the equilibrium level. Based on this, we propose to strengthen institutional innovation and help propel coordinated urban and rural development, in terms of employment, social security, finance, land management and use.
Dissociation cross sections of ground-state and excited charmonia with light mesons in the quark model
Creators: name: Barnes, T.
name: Swanson, E. S.
name: Wong, C. -Y.
name: Xu, X. -M.
Publisher: name: arXiv
Year: 2003
Subjects: subject: Nuclear Theory (nucl-th)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: We present numerical results for the dissociation cross sections of ground-state, orbitally- and radially-excited charmonia in collisions with light mesons. Our results are derived using the nonrelativistic quark model, so all parameters are determined by fits to the experimental meson spectrum. Examples of dissociation into both exclusive and inclusive final states are considered. The dissociation cross sections of several C=(+) charmonia may be of considerable importance for the study of heavy ion collisions, since these states are expected to be produced more copiously than the J/psi. The relative importance of the productions of ground-state and orbitally-excited charmed mesons in a pion-charmonium collision is demonstrated through the $\sqrt {s}$-dependent charmonium dissociation cross sections.
description: 9 pages, 8 figures
Development of Circular Economy of Characteristic Breeding Industry in Guangxi
Creators: name: Lin, Tao
name: Liang, Xian
name: Lin, Tao
name: Liang, Xian
Publisher: name: Unknown
Year: 2012
Subjects: subject: Agribusiness
subject: Breeding industry
subject: Circular economy
subject: Development pattern
subject: Realization path
subject: Guangxi

description: In order to achieve characteristic, high-quality, high-efficiency, low-consumption, healthy and intensive breeding, we use the ecology method to analyze the status quo of development of characteristic breeding industry in Guangxi, from advantages in resources, industrial development, characteristic breeding, and standardized construction. There are some problems existing in the development of characteristic breeding industry in Guangxi: prominent contradiction among human, land and grain; outdated breeding mode; low comprehensive utilization rate of resources; increasingly deteriorating ecological environment. We put forth the following recommendations: based on the ecological and economic principles, introducing “reduce, reuse, recycle" idea of circular economy; striving to choose the development pattern of circular economy adapting to local resource characteristics, planting and breeding habits; in terms of realization path, paying close attention to construction of standardized breeding farm, cultivation of organic fertilizer industry, infrastructure construction, environmental law enforcement, and other parts; reinforcing the policy guidance, adjusting and optimizing industrial structure, strengthening scientific and technological innovation, and advancing industrialization management, to promote steady development of circular economy of characteristic breeding industry in Guangxi, and accelerate the process of rejuvenating province by breeding industry, enriching the people and building up Guangxi.
Distribution of Boeckella poppei (Mrázek, 1901) (Copepoda: Calanoida) on the Livingston Island, Antarctica
Creators: name: Evtimova, Vesela
name: Pandourski, Ivan
name: Kenderov, Lyubomir
Publisher: name: Zenodo
Year: 2021
Subjects: Antarctica
Livingston Island
Boeckella poppei
expansion of distribution areal
Bulgarian Antarctic Base

description: Livingston Island is the second largest island of the South Shetland Archipelago, Maritime Antarctica. Freshwater fauna in the area is scarcely studied. Previous records are limited and include habitats, which are free of permanent ice or snow cover during the austral summer. The calanoid Boeckella poppei was firstly recorded from the island in the 1990s, from the Todorina buza Lake. More recently, the species was also recorded form freshwater lakes on the Byers Peninsula, Western Livingston Island. During the 28th Bulgarian Antarctic Expedition, we confirmed the presence of B. poppei in the Todorina buza Lake. In addition, we recorded the calanoid in temporary pools (i) situated on the permafrost and formed after the retreat of the Perunika Glacier and (ii) at Hannah Point. In the newly- established habitats the species was very abundant. Our results suggest a considerable expansion in the distribution of B. poppei on the Livingston Island, likely owing to recent climate change and the resulting freeing of additional territories of permanent ice cover. 5th Balkan Scientific Conference on Biology, 15-19 April 2021, Plovdiv Bulgaria, Book of Abstracts, © Plovdiv University Press, 2021, eISBN 978-619-202-644-8
description: {"references": ["Ivanov, L.L. (2017). Antarctica: Livingston Island and Smith Island. Scale 1:100000 topographic map. Manfred W\u00f6rner Foundation, ISBN\u00a0978-619-90008-3-0", "Meredith, M. et al. (2019) Polar Regions. In: P\u00f6rtner H.-O. et al. (eds) IPCC Special Report on the Ocean and Cryosphere in a Changing Climate", "Pandourski, I. & Chipev, N. (1999). Morphological variability in a Boeckella poppei Mrazek, 1901 (Crustacea: Copepoda) population from a glacial lake on the Livingston Island (the Antarctic). Bulgarian Antarctic Research: Life Sciences 2, 83-92.", "Toro, M. et al. (2007). Limnological characteristics of the freshwater ecosystems of Byers Peninsula, Livingston Island, in maritime Antarctica. Polar Biology 30, 635", "Walter, T.C. & Boxshall, G. (2021). World of Copepods Database. Boeckella Guerne & Richard, 1889. Accessed on 2021-03-20 through World Register of Marine Species at: http://marinespecies.org/aphia.php?p=taxdetails&id=346853"]}
Integrated Development of Urban and Rural Industries in the Xi'an Metropolitan Area
Creators: name: Zhang, Hong
name: Gao, Zheng
name: Zhang, Hong
name: Gao, Zheng
Publisher: name: Unknown
Year: 2012
Subjects: subject: Agribusiness
subject: Metropolitan area
subject: Urban and rural areas
subject: Industrial integration

description: Based on the diagnosis of the industrial structure in the Xi'an metropolitan area, we point out the problems in the development of urban and rural industries in the Xi'an metropolitan area: there is imbalance in the industrial structure; the planning and layout is chaotic; the service system is unsound; the development of the county economy lags behind. From structural adjustment, urban-rural division of labor, technical support, and the coordination of interests, we put forward the measures for coordinating the development of urban and rural industries.
Pulchrana glandulosa
Creators: name: Figueroa, Alex
name: Low, Martyn E. Y.
name: Lim, Kelvin K. P.
Publisher: name: Zenodo
Year: 2023
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Amphibia
Anura
Ranidae
Pulchrana
Pulchrana glandulosa

description: Pulchrana glandulosa (Boulenger, 1882) — Erroneous.
Rough-sided Frog
Singapore records.
Rana glandulosa —Matsui et al., 2012: 43.—Goldberg et al., 2017: 230.
Remarks. Pulchrana baramica and P. laterimaculata were both previously known in Singapore as P. glandulosa (see accounts above). In comparing the differences between P. baramica and P. laterimaculata with P. rawa, Matsui et al. (2012) also summarised the erection of Pulchrana by Dubois (1992). The authors noted that P. glandulosa was placed into the new genus, and included Singapore in its distribution. As Matsui et al. (2012) also discussed P. baramica and P. laterimaculata from Singapore, it can only be taken that they were referring to P. glandulosa sensu stricto. In fact, Singapore was also listed in the distribution of P. glandulosa on the Amphibian Species of the World database as cited by Goldberg et al. (2017). Nonetheless, P. glandulosa ranges from southern Vietnam west to southern Thailand, and south through Peninsular Malaysia to Sumatra, Natuna Islands., and Borneo, but does not occur in Singapore (Inger 1966; Leong 2001b; Orlov et al. 2002b).
LKCNHM & NHMUK Museum specimens. No specimens.
Additional Singapore museum specimens. No specimens.
description: Published as part of Figueroa, Alex, Low, Martyn E. Y. & Lim, Kelvin K. P., 2023, Singapore's herpetofauna: updated and annotated checklist, history, conservation, and distribution, pp. 1-378 in Zootaxa 5287 (1) on pages 257-258, DOI: 10.11646/zootaxa.5287.1.1, http://zenodo.org/record/7960319
Factors Influencing Willingness and Ability of Farmers to Adopt New Technologies: A Case Study of Guanzhong Area
Creators: name: Tian, Jing-Na
name: Li, Lu-Tang
name: Tian, Jing-Na
name: Li, Lu-Tang
Publisher: name: Unknown
Year: 2012
Subjects: subject: Agribusiness
subject: New technologies
subject: Willingness of adoption
subject: Farmers’ ability
subject: Logit Model

description: Based on data of 248 rural households in Pucheng County and Huxian County, we established the Two-Level Logit Model to analyze the willingness of farmers to adopt new technologies, its influence factors, and probability of successful adoption of new technologies. Results show that the willingness has positive correlation with whether the farmer is head of household, the educational level, occupation, agricultural loan, the number of family labor, and information dissemination channel, while it has negative correlation with non-agricultural employment proportion and whether the farmer is village cadre. In the model of the probability of farmers’ successfully adopting new technologies, occupation, agricultural loan, planting area, gender and educational level are positively correlated, while age and non-agricultural employment proportion are negatively correlated. Large-scale flow of rural labor plays a negative role in popularization of technologies in rural areas through influencing factors, including number of family labor, non-agricultural employment proportion, educational level, gender, and whether the farmer is village cadre. Finally, on the basis of results of empirical study, we put forward countermeasures and suggestions for strengthening ability of farmers to adopt new technologies.