cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Data science training for experimental biology graduate students
Creators: name: Akirtava, Christina
name: Schwartz, Russell
name: Weiss, Emily Daniels
name: Pottmeyer, Laura Ochs
Publisher: name: F1000 Research Limited
Year: 2020

description: The life sciences education community has recognized for more than a decade that education of future biomedical scientists must be reformed to enhance quantitative and computational training needed for modern biomedical research [1]. Considerable effort has been put into defining what quantitative competencies should be expected of aspiring life scientists (e.g., [2, 3]). While we now have a much better idea of what needs to be done and numerous anecdotal successes [4], systematic progress has been slow and has faced many obstacles [5]. We developed a new course to provide working knowledge and skills for experimental biology students, with specific focus on incoming students in the Carnegie Mellon Biological Sciences PhD program. While we and others have previously developed curricula to ensure adequate quantitative training of many cohorts (Biological Sciences undergraduates, Computational Biology students at BS, MS, and PhD levels at CMU [4]), the biology PhD level presents particular challenges. Because of the varied expectations at the undergraduate level, we assume biology PhD students enter with no prior training in biostatistics or bioinformatics. Further, instructional time for PhD students is limited as they are expected to move expeditiously to devoting their efforts primarily to thesis research. We have developed a class to serve this cohort by combining instruction in
cross-cutting methodologies with hands-on work on primary data from department laboratories to exercise these skills and promote transferability to new problem domains.

[1] N. R. Council et al., BIO2010: Transforming undergraduate education for future research biologists. National Academies Press, 2003.
[2] L. Welch et al., “Bioinformatics curriculum guidelines: toward a definition of core competencies,”PLOS Computational Biology, vol. 10, no. 3, 2014.
[3] M. A. W. Sayres et al., “Bioinformatics core competencies for undergraduate life sciences education,”PloS ONE, vol. 13, no. 6, 2018.
[4] N. Mulder et al., “The development and application of bioinformatics core competencies toimprove bioinformatics training and education,”PLoS Computational Biology, vol. 14, no. 2,2018.
[5] J. Williams et al., “Barriers to integration of bioinformatics into undergraduate life sciences education,”BioRxiv, p. 204420, 2017.
Gas cooling in semi-analytic models and SPH simulations: are results consistent?
Creators: name: Saro, A.
name: De Lucia, G.
name: Borgani, S.
name: Dolag, K.
Publisher: name: arXiv
Year: 2010
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: We present a detailed comparison between the galaxy populations within a massive cluster, as predicted by hydrodynamical SPH simulations and by a semi-analytic model (SAM) of galaxy formation. Both models include gas cooling and a simple prescription of star formation, which consists in transforming instantaneously any cold gas available into stars, while neglecting any source of energy feedback. We find that, in general, galaxy populations from SAMs and SPH have similar statistical properties, in agreement with previous studies. However, when comparing galaxies on an object-by-object basis, we find a number of interesting differences: a) the star formation histories of the brightest cluster galaxies (BCGs) from SAM and SPH models differ significantly, with the SPH BCG exhibiting a lower level of star formation activity at low redshift, and a more intense and shorter initial burst of star formation with respect to its SAM counterpart; b) while all stars associated with the BCG were formed in its progenitors in the semi-analytic model used here, this holds true only for half of the final BCG stellar mass in the SPH simulation, the remaining half being contributed by tidal stripping of stars from the diffuse stellar component associated with galaxies accreted on the cluster halo; c) SPH satellites can loose up to 90 per cent of their stellar mass at the time of accretion, due to tidal stripping, a process not included in the semi-analytic model used in this study; d) in the SPH simulation, significant cooling occurs on the most massive satellite galaxies and this lasts for up to 1 Gyr after accretion. This physical process is not included in the semi-analytic model used in our study, as well as in most of the models discussed in the recent literature.
description: Revised version submitted to MNRAS, 15 pages, 9 figures. A High-resolution version of the paper and figures can be found at this http://adlibitum.oats.inaf.it/saro/SAM2/paper.pdf
Saurorhynchus Reis 1892
Creators: name: Maxwell, Erin E.
name: Stumpf, Sebastian
Publisher: name: Zenodo
Year: 2017
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Actinopterygii
Saurichthyiformes
Saurichthyidae
Saurorhynchus

description: Saurorhynchus sp.   Material studied
GERMANY: Numismalismergel jaw (SMNS 96082).  Remark
 SMNS 96082 is the only Pliensbachian record of Saurorhynchus of which we are aware. Although clearly referable to Saurorhynchus, SMNS 96082 is distinct from S. anningae sp. nov. in the shape of the posterior mandible and position of the mandibular sensory canal, and also from S. brevirostris, in that the posterior edge of the mandible is more strongly sinusoidal. However, there are few features to differentiate SMNS 96082 from the Toarcian-aged S. acutus and S. hauffi sp. nov. One notable difference is the development of plicidentine, which is easily visible around all tooth bases in this specimen. In Toarcian saurichthyids, plicidentine, while present at least some of the time, does not appear to be as well-developed or consistently present. However, body size/absolute tooth size may be playing a role: with a mandibular depth of 23 mm, the Numismalismergel jaw ranks among the largest Saurorhynchus skulls from southwestern Germany (Suppl. Table 1; Hauff 1938). As in the Toarcian material, the collar region of the teeth does not appear to be corrugated.
 Comparing the jaw depth to other Toarcian Saurorhynchus skulls, a skull length of between 114 mm (based on PMU 30009) and 143 mm (Hauff 1938) is predicted, which would result in an estimated fork length of 40–50 cm.
description: Published as part of Maxwell, Erin E. & Stumpf, Sebastian, 2017, Revision of Saurorhynchus (Actinopterygii: Saurichthyidae) from the Early Jurassic of England and Germany, pp. 1-29 in European Journal of Taxonomy 321 (321) on pages 20-21, DOI: 10.5852/ejt.2017.321, http://zenodo.org/record/3829282
Complexity-constrained quantum thermodynamics
Creators: name: Munson, Anthony
name: Kothakonda, Naga Bhavya Teja
name: Haferkamp, Jonas
name: Halpern, Nicole Yunger
name: Eisert, Jens
name: Faist, Philippe
Publisher: name: arXiv
Year: 2024
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: Quantum complexity measures the difficulty of realizing a quantum process, such as preparing a state or implementing a unitary. We present an approach to quantifying the thermodynamic resources required to implement a process if the process's complexity is restricted. We focus on the prototypical task of information erasure, or Landauer erasure, wherein an n-qubit memory is reset to the all-zero state. We show that the minimum thermodynamic work required to reset an arbitrary state, via a complexity-constrained process, is quantified by the state's complexity entropy. The complexity entropy therefore quantifies a trade-off between the work cost and complexity cost of resetting a state. If the qubits have a nontrivial (but product) Hamiltonian, the optimal work cost is determined by the complexity relative entropy. The complexity entropy quantifies the amount of randomness a system appears to have to a computationally limited observer. Similarly, the complexity relative entropy quantifies such an observer's ability to distinguish two states. We prove elementary properties of the complexity (relative) entropy and determine the complexity entropy's behavior under random circuits. Also, we identify information-theoretic applications of the complexity entropy. The complexity entropy quantifies the resources required for data compression if the compression algorithm must use a restricted number of gates. We further introduce a complexity conditional entropy, which arises naturally in a complexity-constrained variant of information-theoretic decoupling. Assuming that this entropy obeys a conjectured chain rule, we show that the entropy bounds the number of qubits that one can decouple from a reference system, as judged by a computationally bounded referee. Overall, our framework extends the resource-theoretic approach to thermodynamics to integrate a notion of time, as quantified by complexity.
description: 17 pages (6 figures) + appendices (41 pages)
Variant Calling of the SARS-CoV-2 Genomes using Highly Accurate Long Reads
Creators: name: Tseng, Elizabeth
Publisher: name: F1000 Research Limited
Year: 2020

description: SARS-CoV-2 is a single-stranded, 30 kb RNA virus from the coronavirus family that is currently causing a worldwide pandemic, with over 3 million confirmed cases and 212k deaths as of April 2020. Complete sequencing of the viral genome allows epidemiological tracing and discovery of mutations that may be important for antiviral and vaccine research.Complete and accurate sequencing of the viral genome allows epidemiological tracing and discovery of mutations that may be important for antiviral and vaccine research.

PacBio’s SMRT Sequencing uses circular consensus sequencing that can generate long, highly accurate (HiFi) reads forlong, high-fidelity (HiFi) SARS-Cov-2 genomes. We generated several in-house datasets using amplicon-based approaches with insert sizes ranging from 400 bp to several kb long, as well as hybridization-based approaches that can capture fragments of 5 kb or longer.

We tested several variant calling methods including PacBio’s own MinorVariant (originally developed for HIV quasi-species detection) and LoFreq. We show that regardless of amplicon size, reference-guided mapping approaches can call SNPs accurately at as low as 10-fold coverage under the assumption of a single, consensus genome. Higher coverages are required for identifying minor variants spiked in at 1%, 10%, and 50% frequency.
Chirped pulse control over the melting of superconductors
Creators: name: Recasens, Maria
name: Kasper, Valentin
name: Lewenstein, Maciej
name: Johnson, Allan S.
Publisher: name: arXiv
Year: 2024
Subjects: subject: Superconductivity (cond-mat.supr-con)
subject: Optics (physics.optics)
subject: FOS: Physical sciences

description: Strong field terahertz pulses are increasingly used to excite and control quantum materials at the ultrafast timescale. They have found widespread application by enabling direct addressing of the superconducting gap or Josephson resonances and are essential in Higgs spectroscopy. Large non-linear optical signals can be induced by the strong coupling of the THz and superconducting degrees of freedom. However, far less attention has been paid to the strong bi-directional coupling between field and material this implies. Here, we use the framework of the time-dependent Ginzburg-Landau equations to study the full field and material evolution of a superconductor driven by strong field terahertz pulses. We find that at high field strengths, the backreaction of the superconductor induces large changes to the driving pulse, which in turn leads to a runaway melting of the superconducting condensate. This results in a surprisingly large sensitivity to the initial driving pulse chirp, enabling these purely dynamical changes to result in order of magnitude different levels of melting. We also find large-scale spectral shifting of the driving pulse to occur in just a few hundred nanometers of propagation through a superconductor. We attribute these effects to an inverse plasma redshift, in which the driving field breaks Cooper pairs and decreases the free-electron mobility, analogous to reducing the density of a plasma.
description: 9 pages, 6 figures
PR - FARM LABOR TRENDS IN SOUTHWEST FLORIDA, USA â€“ MANAGEMENT CHALLENGES AND OPPORTUNITIES
Creators: name: Roka, Fritz M.
Publisher: name: Unknown
Year: 2017
Subjects: subject: Labor and Human Capital
subject: H-2A
subject: corporate social responsibility
subject: minimum wage

description: Reliance on foreign guest workers, rising minimum wages, and corporate social responsibility are three trends emerging within the southwest Florida agricultural economy. These trends are creating higher costs and pushing employers into new management relationships with their farm workers. On one hand, higher costs could compromise the competitive position of agricultural operations. One the other hand, new management strategies could increase overall worker productivity and/or create new avenues of market access for their products. The success to which agricultural employers adjust to these trends with cost effective management strategies likely will determine their long term economic sustainability.
description: Twenty-First International Farm Management Congress, Edinburgh, Scotland, July 2-7, 2017
Giant Chromospheric Anemone Jet Observed with Hinode and Comparison with Magnetohydrodynamic Simulations: Evidence of Propagating Alfven Waves and Magnetic Reconnection
Creators: name: Nishizuka, N.
name: Shimizu, M.
name: Nakamura, T.
name: Otsuji, K.
name: Okamoto, T. J.
name: Katsukawa, Y.
name: Shibata, K.
Publisher: name: arXiv
Year: 2008
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: Hinode discovered a beautiful giant jet with both cool and hot components at the solar limb on 2007 February 9. Simultaneous observations by the Hinode SOT, XRT, and TRACE 195 satellites revealed that hot (5x10^6 K) and cool (10^4 K) jets were located side by side and that the hot jet preceded the associated cool jet (1-2 minutes). A current-sheet-like structure was seen in optical (Ca IIH), EUV (195A), and soft X-ray emissions, suggesting that magnetic reconnection is occurring in the transition region or upper chromosphere. Alfven waves were also observed with Hinode SOT. These propagated along the jet at velocities of 200 km/s with amplitudes (transverse velocity) of 5-15 km/s and a period of 200 s. We performed two-dimensional MHD simulation of the jets on the basis of the emerging flux-reconnection model, by extending Yokoyama and Shibata's model. We extended the model with a more realistic initial condition (10^6 K corona) and compared our model with multiwavelength observations. The improvement of the coronal temperature and density in the simulation model allowed for the first time the reproduction of the structure and evolution of both the cool and hot jets quantitatively, supporting the magnetic reconnection model. The generation and the propagation of Alfven waves are also reproduced self-consistently in the simulation model.
description: 12 pages, 3 figures
Minor-embedding in adiabatic quantum computation: II. Minor-universal graph design
Creators: name: Choi, Vicky
Publisher: name: arXiv
Year: 2010
Subjects: subject: Quantum Physics (quant-ph)
subject: Computational Complexity (cs.CC)
subject: FOS: Physical sciences
subject: FOS: Computer and information sciences

description: In [Choi08], we introduced the notion of minor-embedding in adiabatic quantum optimization. A minor-embedding of a graph G in a quantum hardware graph U is a subgraph of U such that G can be obtained from it by contracting edges. In this paper, we describe the intertwined adiabatic quantum architecture design problem, which is to construct a hardware graph U that satisfies all known physical constraints and, at the same time, permits an efficient minor-embedding algorithm. We illustrate an optimal complete-graph-minor hardware graph. Given a family F of graphs, a (host) graph U is called F-minor-universal if for each graph G in F, U contains a minor-embedding of G. The problem for designing a F-minor-universal hardware graph U_{sparse} in which F consists of a family of sparse graphs (e.g., bounded degree graphs) is open.
description: 10 pages, 5 figures
Derivation of Lüscher's finite size formula for $Nπ$ and $NN$ system
Creators: name: Ishizuka, N.
Publisher: name: arXiv
Year: 2009
Subjects: subject: High Energy Physics - Lattice (hep-lat)
subject: FOS: Physical sciences

description: I present derivation of Lüscher's finite size formula for the elastic $Nπ$ and the $NN$ scattering system for several angular momenta from the relativistic quantum field theory.
description: 8 pages, Poster at Lattice 2009(Hadron Spectroscopy), to be published in PoS(LAT2009)119
Quantum stochastic differential equations and continuous measurements: unbounded coefficients
Creators: name: Santis, Ricardo Castro
name: Barchielli, Alberto
Publisher: name: arXiv
Year: 2010
Subjects: subject: Probability (math.PR)
subject: Mathematical Physics (math-ph)
subject: FOS: Mathematics
subject: FOS: Physical sciences

description: A natural formulation of the theory of quantum measurements in continuous time is based on quantum stochastic differential equations (Hudson-Parthasarathy equations). However, such a theory was developed only in the case of Hudson-Parthasarathy equations with bounded coefficients. By using some results on Hudson-Parthasarathy equations with unbounded coefficients, we are able to extend the theory of quantum continuous measurements to cases in which unbounded operators on the system space are involved. A significant example of a quantum optical system (the degenerate parametric oscillator) is shown to fulfill the hypotheses introduced in the general theory.
description: 28 pages
Deliverable D7.6 IP4MaaS leaflet, version 2
Creators: name: van Hek, Charlotte
name: Rizzi, Giuseppe
Publisher: name: Zenodo
Year: 2023

description: This deliverable describes and shows the second version of the Project Leaflet developed by the IP4MaaS project. In this document we describe the objectives of the leaflet, as well as the structure and design. This second leaflet, delivered at the end of the project, is the second out of two. A first leaflet was developed in the first stage of the project.
Single cell chromatin accessibility delineates cellular identities of the neonatal organ of corti
Creators: name: Shuze Wang
name: Joerg Waldhaus
name: Liu, Jie
name: Lee, Mary
name: Yujuan Fu
name: Jones, Scott
Publisher: name: F1000 Research Limited
Year: 2020

description: The organ of Corti, the receptor organ for hearing, is formed by a variety of sensory hair cells (HCs) and supporting cells (SCs) within the cochlea. However, the gene regulation mechanisms of cochlea development are not fully understood.

The aim of this study is to identify regulatory elements controlling differentiation and maturation of the organ of Corti. To achieve this goal, we generated scATAC-seq and scRNA-seq libraries from postnatal day 2 organ of Corti preparations divided into apical and basal compartments. By integrating scRNA-seq data, we identified cell types of scATAC-seq by calculating a Jaccard similarity matrix, identified cell type specific transcription factors (TFs), classified them as activators and repressors based on function, and further validation by footprints.

Focusing on HCs, we reconstructed the organ’s one-dimensional architecture from both scRNA-seq and scATAC-seq data. We identified novel differentially expressed genes along the tonotopic axis and validated them by RNAscope. Additionally, we identified TFs that drive HC differentiation and maturation by reconstructing developmental trajectories.

The results of this study enable us to understand how epigenomic landscape delineates cellular identities and function within the organ of Corti. Further studies will investigate regulatory elements driving SC maturation,which will contribute to regenerative strategies.
Playing nonlocal games across a topological phase transition on a quantum computer
Creators: name: Hart, Oliver
name: Stephen, David T.
name: Williamson, Dominic J.
name: Foss-Feig, Michael
name: Nandkishore, Rahul
Publisher: name: arXiv
Year: 2024
Subjects: subject: Quantum Physics (quant-ph)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: Many-body quantum games provide a natural perspective on phases of matter in quantum hardware, crisply relating the quantum correlations inherent in phases of matter to the securing of quantum advantage at a device-oriented task. In this paper we introduce a family of multiplayer quantum games for which topologically ordered phases of matter are a resource yielding quantum advantage. Unlike previous examples, quantum advantage persists away from the exactly solvable point and is robust to arbitrary local perturbations, irrespective of system size. We demonstrate this robustness experimentally on Quantinuum's H1-1 quantum computer by playing the game with a continuous family of randomly deformed toric code states that can be created with constant-depth circuits leveraging mid-circuit measurements and unitary feedback. We are thus able to tune through a topological phase transition - witnessed by the loss of robust quantum advantage - on currently available quantum hardware. This behavior is contrasted with an analogous family of deformed GHZ states, for which arbitrarily weak local perturbations destroy quantum advantage in the thermodynamic limit. Finally, we discuss a topological interpretation of the game, which leads to a natural generalization involving an arbitrary number of players.
description: 4.5 pages, 3 figures
The Revolutionary Intertextuality of Molora by Yäel Farber
Creators: name: Zinato, Susanna
Publisher: name: Fondazione Università Ca’ Foscari Venezia, Italia
Year: 2021

description:

This article focuses on the challenging intertextual phenomenology characterising the play Molora by South African playwright and director of international acclaim Yäel Farber. Premiered in Grahamstown in 2003, and published in 2008 after award-winning national and international tours, Molora is a radical adaptation of Aeschylus’ Oresteia. It dramatises the challenges faced by South Africa in the highly-charged post-Apartheid aftermath, through dramatic confrontations between Klytemnestra, Elektra, and Orestes echoing the testimonies delivered by perpetrators and victims on the TRC’s ‘stage’, and through a chorus made up of seven Xhosa matriarchs belonging to the Ngquoko split-tone singers, who witness, comment on and significantly participate in the play’s action. Molora’s complex intertextual construction and dynamic are shown to call for a hermeneutical approach careful to avoid simplifying presentifications, as well as any possible fracture with extratextuality. Intertextuality, in fact, is here given the task to creatively and syncretically combine the ancient Greek text with the indigenous Xhosa text through a process of transcultural imbrication that, from beginning to end, exudes the tragedies of all-too-present history while instantiating a revolutionary use of memory.

description: Annali di Ca’ Foscari. Serie occidentale
The Structure of Physical Crystalline Membranes within the Self-Consistent Screening Approximation
Creators: name: Gazit, Doron
Publisher: name: arXiv
Year: 2009
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Soft Condensed Matter (cond-mat.soft)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: The anomalous exponents governing the long wavelength behavior of the flat phase of physical crystalline membranes are calculated within a self-consistent screening approximation (SCSA) applied to second order expansion in 1/d_C (d_C is the co-dimension), extending the seminal work of Le Doussal and Radzihovsky [Phys. Rev. Lett. 69, 1209 (1992)]. In particular, the bending rigidity is found to harden algebraically in the long wavelength limit with an exponent eta=0.789..., which is used to extract the elasticity softening exponent eta_u=0.422..., and the roughness exponent zeta=0.605.... The scaling relation eta_u=2-2eta is proven to hold to all orders in SCSA. Further, applying the SCSA to an expansion in 1/d_C, is found to be essential, as no solution to the self-consistent equations is found in a two bubble level, which is the naive second order expansion. Surprisingly, even though the expansion parameter for physical membrane is 1/d_C=1, the SCSA applied to second order expansion deviates only slightly from the first order, increasing zeta by mere 0.016. This supports the high quality of the SCSA for physical crystalline membranes, as well as improves the comparison to experiments and numerical simulations of these systems. The prediction of SCSA applied to first order expansion for the Poisson ratio is shown to be exact to all orders.
description: Accepted for publication in Physical Review E. Added an exact calculation of the Poisson ratio. 6 pages, 2 figures
Update on Protein Functional Annotation in UniProt in 2020
Creators: name: EL-SAIDI, Rabie
name: Zellner, Hermann
name: Martin, Maria
Publisher: name: F1000 Research Limited
Year: 2020

description: With the increasing number of data generated by sequencing projects, researchers need reliable systems to provide the functional annotation of proteins. UniProtKB is using two functional annotation systems, UniRule and ARBA (Association-Rule-Based Annotator), to automatically annotate UniProtKB/TrEMBL in an efficient and scalable manner with a high degree of accuracy. These systems use protein signatures and taxonomy classifications to infer the biochemical features and biological functions of proteins. This knowledge is expressed in the form of rules: sets of IF-THEN statements coming from expert curation (UniRule [1]) or generated by machine learning (ARBA [2]). Rules are applied at each release keeping the propagated annotations up-to-date. On the UniProtKB website, information added by annotation rules is clearly highlighted as such using evidence tags. These tags can also be used as keywords to search for or filter out annotation added by a rule. The protein function community could also benefit from those rules, as some sequences may not be yet available in public databases or could be present in highly redundant proteomes absent from UniProtKB. This has been made possible via UniFIRE (The UniProt Functional annotation Inference Rule Engine), an engine to execute rules in the URML (UniProt Rule Markup Language) format.
RNA-Scoop: interactive visualization of isoforms in single-cell transcriptomes
Creators: name: Stephenson, Maria
name: Nip, Ka Ming
name: Hafezqorani, Saber
name: Yang, Chen
name: Gagalova, Kristina
name: Warren, René
name: İnanç Birol
Publisher: name: F1000 Research Limited
Year: 2020

description: Isoform detection and discovery in single cells is central to improving our understanding of tumor heterogeneity. However, since current interactive RNA-seq visualization tools are designed for bulk RNA-Seq data, they have limited utility in displaying and analyzing single-cell RNA-seq data. Here, we introduce RNA-Scoop, a tool which visualizes isoform expression in single cells through an interactive t-SNE plot.

The input of RNA-Scoop consists of a single JSON file, which specifies the paths to a GTF file containing the isoforms of interest, a matrix file containing their expression levels in each cell, and files containing labels for the matrix rows and columns. Users can select genes for the isoform view, where all isoforms of selected genes are displayed. The t-SNE plot allows users to zoom in and out of different areas and select cells via lasso selection. Upon selection, displayed isoforms are colored according to their average level of expression in the selected cells. Expression per cluster is visualized through a dot plot. Additionally, isoforms are selectable, enabling users to highlight the cells in which isoforms of interest are expressed. Through these easy-to-use features, RNA-Scoop simplifies the interrogation of isoforms and cell types in thousands of cells.
An N-dimensional version of the Beurling-Ahlfors extension
Creators: name: Kovalev, Leonid V.
name: Onninen, Jani
Publisher: name: arXiv
Year: 2009
Subjects: subject: Complex Variables (math.CV)
subject: FOS: Mathematics
subject: 30C65, 47H05, 47B34

description: We extend monotone quasiconformal mappings from dimension n to n+1 while preserving both monotonicity and quasiconformality. The extension is given explicitly by an integral operator. In the case n=1 it yields a refinement of the Beurling-Ahlfors extension.
description: 9 pages. Added references, edited concluding remarks
Probabilistic factor graph modeling and analysis of biological networks
Creators: name: Kotiang, Stephen
name: Eslami, Ali
Publisher: name: F1000 Research Limited
Year: 2020

description: In this work, we present a probabilistic graphical model that is aimed to quantify how well the existing state-of-the-art biological networks correspond to the measured gene expression data. The model is formulated as a bipartite graph representation of molecular networks and is employed to explore the allowable stable states in two experimentally verified gene networks in E. coli.
Mixture modeling for genetic regulatory networks from single perturbation gene expression experiments
Creators: name: Burton, David S
name: McCall, Matthew
Publisher: name: F1000 Research Limited
Year: 2020

description: A sparse set of slides on a new method for scoring networks using a likelihood based on mixture modeling. This is a further application of the probability of expression method (Parmagiani and Garreth, 2002). We are applying the method on ddCT (Pfaffl, 2001) values from single perturbation gene expression experiments on murine colon cancer cell lines.
Wikidata WikiProject COVID-19 : a community effort to integrate biomedical knowledge
Creators: name: Lubiana, Tiago
Publisher: name: F1000 Research Limited
Year: 2020

description: The Wikidata WikiProject COVID-19 is a collaborative, multinational effort created in the current pandemic to improve the representation of pandemic-related content on Wikidata. One of the core goals of the project is reconciling into Wikidata a range of COVID-19 related datasets. The project has integrated pieces of information from critical datasets on epidemiology, on SARS-COV-2 proteins, macromolecular complexes, and protein-protein interactions, on cell lines used in SARS-CoV-2 research, and datasets descriving COVID-19 related scholarly articles themselves. This integrated information is available openly and can be queried via a SPARQL endpoint. The data is accessible in a web-based format via the Wikidata API and wrapper packages in Python and R. The contributions of the WikiProject COVID-19 participants have led to a powerful resource for the life sciences community to parse our collective knowledge about the pandemic.
Minimal Elements of the Causal Boundary with Applications to Spacetime Splitting
Creators: name: García-Heveling, Leonardo
Publisher: name: arXiv
Year: 2024
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: Mathematical Physics (math-ph)
subject: Differential Geometry (math.DG)
subject: FOS: Physical sciences
subject: FOS: Mathematics
subject: 53C50 (Primary), 83C75 (Secondary)

description: In 1972, Geroch, Kronheimer, and Penrose introduced what is now called the causal boundary of a spacetime. This boundary is constructed out of Terminal Indecomposable Past sets (TIPs) and their future analogues (TIFs), which are the pasts and futures of inextendible causal curves. The causal boundary is a key tool to understand the global structure of a spacetime. In this paper, we show that in a spacetime with compact Cauchy surfaces, there is always at least one minimal TIP and one minimal TIF, minimal meaning that it does not contain another TIP (resp.\ TIF) as a proper subset. We then study the implications of the minimal TIP and TIF meeting each other. This condition generalizes some of the "no observer horizon" conditions that have been used in the literature to obtain partial solutions of the Bartnik splitting conjecture. We also show that such a no observer horizons condition is satisfied when the spacetime has a (possibly discrete) timelike conformal symmetry, generalizing a result of Costa e Silva, Flores, and Herrera about conformal Killing vector fields.
description: 15 pages, 2 figures. Changes in v4: small changes in the introduction, added Remark 3.2. Final version
A DECISION TREE APPLICATION IN TOURISM BASED REGIONAL ECONOMIC DEVELOPMENT
Creators: name: Curtis, Panayiotis
name: Kokotos, Dimitris
Publisher: name: tourismos
Year: 2009

description: The reasons for the deficient performance of Ionian Islands tourism in terms of in coming revenues expressed in USD and return on equity capital invested on hotels is explored. The answers to the questioner of management of the hotels surveyed were analyzed with the use of the Decision Tree tool. The issue of competitiveness of the tourism product was assessed. The development of alternative forms of tourism is proposed as a means of improving competitiveness and restoring sustainability in the sector.
description: tourismos, Vol. 4 No. 2 (2009)
PR - PRODUCTIVITY BY AGE OVER EIGHT U.S. CENSUS YEARS
Creators: name: Tauer, Loren W.
Publisher: name: Unknown
Year: 2017
Subjects: subject: Productivity Analysis
subject: farmer age
subject: farmer productivity

description: The productivities of farmers by age group for each of the previous eight U.S. agricultural census years were estimated by Tornqvist productivity indices. Productivity increases with age, peaks at midâ€life and then decreases by age for each census year. This concave productivity pattern appears to be muted in the last census years of 2007 and 2012, such that the productivity increase and then decrease is not as large as in previous census years. If older farmers had not experienced decreases in productivity, U.S. agricultural output in 2012 would have been 5.66 percent greater.
description: Twenty-First International Farm Management Congress, Edinburgh, Scotland, July 2-7, 2017
Furio Jesi Translation Theorist
Creators: name: Dogà, Ulisse
Publisher: name: Fondazione Università Ca’ Foscari Venezia, Italia
Year: 2021

description:

The figure of the cultural anthropologist Furio Jesi has experienced a major rediscovery in recent years thanks to the commendable republication of his books and the publication of numerous unpublished works. In this rediscovery, however, a non-secondary aspect of this multifaceted author still remains in shadow, namely his philosophical and hermeneutic interest in the idea of translation. There are many traces of Jesi’s interest in the theory of translation. A volume entitled Translation and Duplicity of Languages was not completed, but there are some chapters from this project (already published in magazines) and materials still awaiting publication. After the study of Walter Benjamin’s Essays on Language, translation represents for Jesi a fundamental ‘linguistic’ junction of the relationship between the sacred and the profane, between myth and mythologem, between the origin and history of language. The aim of this essay will be to reconstruct and clarify Jesi’s idea of ‘translatability’, trying to trace a common thread among the theoretical essays in which Jesi determines translation as a further gnoseological background of his ‘mythological machine’ on the one hand, and the excursus of history of the language and his critical essays on literature on the other.

description: Annali di Ca’ Foscari. Serie occidentale
Long lived matter waves Bloch oscillations and dynamical localization by time dependent nonlinearity management
Creators: name: Bludov, Yuliy V.
name: Konotop, Vladimir V.
name: Salerno, Mario
Publisher: name: arXiv
Year: 2009
Subjects: subject: Other Condensed Matter (cond-mat.other)
subject: FOS: Physical sciences

description: We introduce a new method to achieve long lived Bloch oscillations and dynamical localization of matter wave gap solitons in optical lattices. The method is based on time dependent modulations of the nonlinearity which can be experimentally implemented by means of the Feshbach resonance technique. In particular, we show that the width of the wave packet is preserved if time modulations of the nonlinearity are taken proportional to the curvature of the linear band spectrum which for most typical experimental settings are well approximated by harmonic time modulations of proper frequencies.
IDENTITY AND SEX: CONCURRENT ASPECTS OF GAY TOURISM
Creators: name: Monterrubio, Carlos
Publisher: name: tourismos
Year: 2009

description: The present article aims to contribute to the recognition of two relevant aspects in gay travel; identity and sex. The paper explores the existing published work related to the relationships between tourism, gay men and identity. It concludes that the issue of identity commonly plays a crucial role as a travel reason in gay tourism. Also, it analyses the research evidence to suggest that sex is a frequentlypresent phenomenon in gay travel. By critically analysing the available research, the paper presents evidence to suggest that both aspects are relevant in the gay tourism spectrum.
description: tourismos, Vol. 4 No. 2 (2009)
THE LIFE CYCLE OF AGRO TOURIST ENTERPRISES
Creators: name: Dritsaki, Chaido
Publisher: name: tourismos
Year: 2009

description: This paper analyzes the supply of an important form of non urban tourism, the socalled agro tourism, together with providing a detailed literature review of the various stages of a tourist product life cycle. A theoretical econometric model of these life cycle phases is then presented. Finally, suggestions are proposed about the contribution of private and public sectors, and the strategies political institutions should follow in order to sustain and promote agro tourism.
description: tourismos, Vol. 4 No. 2 (2009)
Gargela polyacantha W. Li 2019
Creators: name: Léger, Théo
Publisher: name: Zenodo
Year: 2024
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Lepidoptera
Crambidae
Gargela
Gargela polyacantha

description: Gargela polyacantha Li, 2019
Figs. 30, 89, 147.
Gargela polyacantha W. Li in Yang et al., 2019, pp. 2200–2102, figs. 1, 2, 5, 6. Type locality: China, Yunnan Province, Xishuangbanna Dai Autonomous Prefecture, Mengla County, 21°29´N, 101°33´N
MATERIAL
1 ♂, 3 ♀ (detailed information in Table S1; https://doi.org/ 10.5061/dryad.b8gtht7mh).
SIMILAR SPECIES
Gargela minuta Song et al., 2009.
DIAGNOSIS
In Gargela polyacantha, the median line is regularly arched and predominantly ocher (Fig. 30), while it is S-shaped and dark brown in Gargela minuta and G. acutibrachium sp. n. In male genitalia (Fig. 89), the medial dorsal bump of the costal process is less pronounced than in Gargela minuta; the distal part is abutted to the valva, while it is separated from it in Gargela minuta. In female genitalia (Fig. 147), the basal half of ductus bursae is covered with dense tiny spines, and the corpus bursae is globular with two thorn-shaped signa (Yang et al., 2019).
DISTRIBUTION
CHINA: Guizhou, Yunnan. PHILIPPINES: Luzon (Batangas, Zambales). Collected at altitudes between 150 and 250 m.
DNA BARCODING
The highest intraspecific p-distance of 0.8% is found between specimens MFNLEP-PYRALPHIL09-D09 and MFNLEP-PYRALPHIL08-H05, both from Zambales mountains in Luzon.
REMARKS
This is the first record of this species from the Philippines.
description: Published as part of Léger, Théo, 2024, Half of the Diversity Undescribed: Integrative Taxonomy Reveals 32 New Species and a High Cryptic Diversity in the Scopariinae and Crambinae of the Philippines (Lepidoptera: Crambidae), pp. 1-93 in Bulletin of the Society of Systematic Biologists 3 (2) on page 42, DOI: 10.18061/bssb.v3i2.9527, http://zenodo.org/record/15116964
DRAMATIC CHANGES IN THE CONTINUOUSLY EVOLVING TOURIST DESTINATIONS: THE CASE OF PARALIA IN PIERIA
Creators: name: Zografos, George
name: Deffner, Alex
Publisher: name: tourismos
Year: 2009

description: This paper examines the evolution of ‘Paralia’ as a key mass tourism destination in northern Greece. The paper analyses the changes which are brought to a destination as a result of its main markets’ current socio-economic situation. Thus, it draws conclusions about the vulnerability of destinations, and how trends in key markets can move destinations to the various stages of the so-called Destination’s Life Cycle. The primary data are derived from a questionnaire survey addressed to citizens. The results of the survey seem to verify previous analyses about the area. Local people tend to compromise with the current situation. At the end, courses of action are suggested which could help the destination to move away from insecurity and stagnation. Proposals based on the outline of the destination’s strengths and weaknesses, opportunities and threats include the organisation of special events throughout the year and incentives for the attraction of residents from neighbouring urban centres.
description: tourismos, Vol. 4 No. 2 (2009)
title: Characterisation of the mitotic Kinesin 13-1 in Trypanosoma brucei
Creators: name: Riemer, Anna
Publisher: name: University of Bayreuth
Year: 2018
Subjects: subject: Trypanosoma brucei
subject: Kinesin
subject: microtubule depolymerisation
subject: ATPase activity
subject: 570

description: Trypanosoma brucei is a unicellular, uniflagellated parasite causing sub-Saharan African trypanosomiasis, commonly known as sleeping sickness. In the effort to eradicate this disease, finding new drugs that are without severe side effects for patients and easy to administer, is a challenging task. This thesis assesses the mitotic kinesin TbKif13-1 as potential drug target. Attempts were made to establish the prerequisites for an in vivo and an in vitro TbKif13-1 high-throughput inhibitor screen with automated image analysis. The basis for both assays was the TbKif13-1 mediated microtubule depolymerisation and its prevention by an appropriate inhibitor. In the in vivo assay, the substrate was the interphase microtubulule cytoskeleton of HeLa cells. The prerequisite for this assay is a stable HeLa cell line exhibiting a depolymerised microtubule cytoskeleton after inducible overexpression of eGFPTbKif13-1 S143A. The mutation prevents its inhibition by phosphorylation. The basic idea worked well in transiently transfected HeLa cells. However, generated stable cell lines did not show microtubule cytoskeleton depolymerisation after eGFPTbKif13-1 S143A overexpression. In the in vitro assay, the depolymerisation substrate for recombinantly purified His6TbKif13-1 were T. brucei cytoskeletons. The assay worked well on microscopy slides. However, it did not work in the prerequisited format, 384-well plates.
In this thesis functional characterisation of TbKif13-1 domains occurred, using TbKif13-1 deletion constructs for T. brucei in vivo and in vitro assays. Immunfluorescence studies indicated that the intranuclear TbKif13-1 localisation depends on a balance of several NLS and NES, with the strongest NLS in the C-terminus. TbKif13-1 was proteasome-dependent degraded and was not found in G1 cells. Degradation signals were supposed within its N- and C-terminus. Full-length TbKif13-1 bound in mitotic cytoskeleton samples in a shape resembling the mitotic spindle. In vitro it bound to and depolymerised taxol-stabilised microtubules in an ATP-dependent manner. The neck-motor domain in conjunction with the C-terminus was found to be its minimal functional construct for in vitro microtubule binding and depolymerisation. The decoupled mechanism of depolymerisation and ATPase activity is conserved in TbKif13-1. Ectopic expression of full-length TbKif13-1 led to reduced growth, zoid formation and defects in spindle formation. This dominant-negative phenotype was strongest after ectopic expression of the neck-motor domain. An expected inhibitory regulation of TbKif13-1´s depolymerisation activity by TbAuk1 mediated phoshorylation could not be confirmed.
CLIMATE CHANGE AND SUSTAINABLE PRACTICES: A CASE STUDY OF THE RESORT INDUSTRY IN FLORIDA
Creators: name: Richins, Harold
name: Scarinci, Janice
Publisher: name: tourismos
Year: 2009

description: Climate change and potential global warming has become important in many forums both nationally and internationally. Though there has previously been some opposition to the existence of human caused climate change and resulting global warming as a threat to the earth’s population and survival, scientific evidence has more recently been found to be compelling. One of the key industries that may be affected by global warming and climate change is the tourism industry. This is becoming a growing concern in Florida, U.S.A. where potential rising sea levels may have a profound effect. This paper discusses the development, importance and implications of climate change, its relationship to the tourism and hospitality industry and provides a case study of the Florida lodging industry regarding mechanisms and responses that the lodging and resort sector of the industry has been taking in addressing climate change factors.
description: tourismos, Vol. 4 No. 2 (2009)
Air transportation and the human environment
Creators: name: Wellings, Rory William
Publisher: name: University of British Columbia
Year: 2011

description: The objective of this study is to investigate the existing air and noise pollution abatement legislation in Canada as it relates to the air transportation industry, and suggest methods of improving this legislation to meet the future needs and demands of the human environment. A second objective is to provide guidelines for business and government action in the future, and to acquaint the individual with some of the issues of the "environmental era of air transportation." Based on personal interview, an extensive literature search, and the application of business principles, this study addresses the technical, economic and social problems associated with the formulation and implementation of effective environmental legislation. In addition, it discusses the roles of business and government in each of these problem areas. The thesis concludes that the Canadian legal system must undergo structural change to accommodate environmental issues; a 1973 Noise Control Act should be passed; and a federally supported environmental education program should be instituted. Other conclusions include recommendations for increased research on the effects of the sonic boom and inadvertent climate modification, increased international participation in environmental affairs, and an improved market system to reflect environmental goods as scarce resources. This thesis also recommends increased government-industry cooperation in the formulation of technical and nontechnical standards and legislation, to ensure that reasonable and specific criteria are established for noise and air pollution abatement. The most important recommendation of this thesis is that a macro system approach be adopted in environmental management. This approach, which recognizes interactions and feedback in the social, economic and political environment, is vital to the future of Air Transportation and the Human Environment.