32151 research outputs found
Sort by
A Brazilian bioregionalization reappraisal based on Angiosperm distribution : a biogeographical and conservation overview
Get PDFFunding: LL thanks CAPES for the funding (Proc. 88887.910185/2023-00) and PTS thanks CNPq (Proc. PQ313151/2023-7) and FAPESP (Proc. 2023/12044-4) for research grants.Bioregionalizations constitute an important tool to synthesize biodiversity knowledge, essential for conservation planning. Bioregions currently recognized in the Neotropics have been delineated using different methods and biologicalgroups, frequently suggesting conflicting results. This study aimed to reevaluate the circumscription of bioregions using the distribution of angiosperm species. Angiosperm records were compiled from online herbaria and filtered fortaxonomical and geographical accuracy according to Flora e Funga do Brasil. A network analysis was performed with InfoMap Bioregions and similarity amongst recognized bioregions was evaluated with an Unweighted Pair Group Method with Arithmetic Mean. Beta diversity patterns were modelled using Generalized Dissimilarity Modelling (GDM) and five climatic variables. A conservation overview was constructed comparing sampling, conservation coverage, deforestation and fire occurrence across bioregions. Seven bioregions were identified and hierarchically clustered: Brazilian subregion (subdivisions not recovered in our analysis); Chacoan subregion, comprised of the Chacoan dominion (four provinces) and the Paraná dominion (two provinces). GDM recognized other heterogeneous areas within these bioregions. The Paraná dominion presented the largest historical anthropization, the Chacoan dominion presented the highest density of fire spots, and the Brazilian subregion had the highest coverage of conservation units while encompassing unknown biodiversity.Peer reviewe
Evaluation of Bayesian network scoring functions in polychotomous data analysis
Get PDFFunding; The authors acknowledge Research Computing at the James Hutton Institute for providing computational resources and technical support for the “UK’s Crop Diversity Bioinformatics HPC” (BBSRC grants BB/S019669/1 and BB/X019683/1), use of which has contributed to the results reported within this paper.Bayesian networks (BNs) are probabilistic graphical models used to represent dependencies and independencies among variables. They have been applied widely to many areas in, e.g., biology and medicine, to untangle complex interrelationships, and are now finding wider use in areas such as social science with differing data features, for example highly polychotomous (multi-category) data. To construct BNs, scoring functions guide selection of the most appropriate model. Among these, the BDe scoring function requires specifying hyperparameters that influence the priors on the network parameters. This study evaluates the performance of four scoring functions—AIC, BIC, BDe, and log-likelihood—particularly with highly polychotomous data. We assessed the overall performance of the scoring function, and for BDe, we varied its hyperparameter to evaluate its impact. Performance of the scoring functions was significantly influenced by the number of nodes, network complexity, and sample size. BIC and BDe (with default hyperparameters) generally offered higher precision, especially with larger sample sizes, while log-likelihood tended to overfit, showing high recall but low precision. AIC and BDe required careful tuning based on discrete levels and sample sizes. Optimizing the hyperparameters in BDe was crucial for balancing model complexity and fit. We propose a simulation method for identifying the optimum hyperparameters for using BDe scoring function in real-world data applications. The study provides insights to enhance BN models’ robustness and accuracy, emphasizing the importance of considering sample size and the number of discrete levels when selecting and tuning scoring functions for BN structure learning.Peer reviewe
Unveiling asymmetric topological photonic states in anisotropic 2D perovskite microcavities
Get PDFFunding: P.G.S. and G.P. acknowledge the support of Innovation Program for Quantum Science and Technology (2023ZD0300300), Westlake University project No. 041020100118 and Zhejiang Provincial Natural Science Foundation (XHD24A2401). L.M. and P.G.S. acknowledge financial support from the Horizon EIC-2022-Pathfinderchallenges-01 Heisingberg project 101114978. A.V.K. acknowledges the Saint Petersburg State University for the Research Grant No. 125022803069-4. H.O. acknowledges support from the Leverhulme Trust through grant No. RPG-2022-188. C.C.S. acknowledges support by the Ministry of Science and Higher Education of the Russian Federation (Megagrant no. 075-15-2022-1112) and from the Special Account for Research Funding of the University of Crete (grants KA10330 and KA10652).Photonic Rashba-Dresselhaus coupling in anisotropic microcavities offers a compelling platform for realizing unconventional topological states with non-zero Berry curvature. In this study, we explore a self-assembled two-dimensional hybrid structure composed of anisotropically oriented organic/inorganic halide perovskite layers confined within a microcavity. The strong optical anisotropies of these perovskite systems, driven by significant refractive index contrasts and robust excitonic resonances at room temperature, enable the emergence of synthetic magnetic fields that mediate photonic and polaritonic interactions. The interplay between polarization-dependent modes and spatial inversion symmetry breaking gives rise to strong photonic Rashba-Dresselhaus spin-orbit coupling, leading to distinct modifications in band topology and energy dispersions. These effects result in the formation of unconventional topological features, including non-zero Berry curvature and off-axis diabolical points, within the photonic and polaritonic bands at room temperature. Our findings reveal the critical role of optical and geometric anisotropies in engineering synthetic gauge fields for light, providing a versatile approach for designing photonic systems with novel topological properties. By leveraging the unique properties of halide perovskites and their ability to support both room-temperature excitons and large birefringence, this work advances the development of polaritonic platforms for applications in topological photonics and spinoptronics.Peer reviewe
Inclusion of patient-centered, non-microbiological endpoints and biomarkers in tuberculosis drug trials
Get PDFTuberculosis drug trials are primarily designed to identify antibiotic regimens with the strongest potency to kill Mycobacterium tuberculosis. However, microbiologic cure is not synonymous with improved health and recovery. Beyond antimicrobial efficacy, parameters such as morbidity and mortality related to lung function, cardiovascular health, and cancer should be prioritized. This narrative review emphasizes the critical need to emphasize clinical outcomes as much, if not more, than microbiological endpoints. We examine the underlying pathophysiological mechanisms and determinants of non-microbiological outcomes in tuberculosis, providing a synthesis of current knowledge. While there is growing evidence for some biomarkers to risk stratify TB patients for risk of all-cause mortality, relapse, or lung damage, no evidence was found on TB-associated cancer or cardiovascular disease. In addition to monitoring microbiologic outcomes, clinical trials and treatment cohorts need to capture patient-centered health dimensions more broadly. Finally, we highlight key research gaps and opportunities to evaluate non-microbiological biomarkers, aiming to improve patient monitoring and enable stratified approaches to tuberculosis management.Peer reviewe
A developmentalist’s view of inheritance
Get PDFRecent years have witnessed the emergence of extensive new data suggesting a different view of inheritance from the view that has dominated biology for over a century. It suggests that what is transmitted across generations are the developmental means to construct phenotypes predicted to match anticipated environmental conditions. Those ‘developmental means’ include genes, but also other resources that parents bequeath to descendants, as well as activities parents engage in to construct the environmental context in which their offspring develop. If there are similarities between the traits of parents and offspring it is because, within lineages, phenotypes are reliably re-constructed across generations. Extra-genetic inheritance processes do an important job in evolution, but that job is, in the main, distinct from that of genetic inheritance. They are best regarded – not as noise, fine-tuning or baroque “add ons” (Wray et al. 2014) – but as essential tools for short-term, rapid-response adaptation. The true function of heredity is to make an informed forecast.Peer reviewe
Teacher identity in English medium instruction : a scoping review of the literature on EMI in the EU
Get PDFEnglish medium instruction (EMI) has steadily increased in higher education institutions across Europe since the Bologna Process in 1999. Most research in this area has focused on teaching practices and learning affordances; however, attention to teacher identity has often been an afterthought. In this article, we conducted a scoping literature review of 23 empirical studies in EMI teacher identity. Arksey and O'Malley (2005) was used alongside Levac et al.'s (2010) recommendations to ensure consistency and replicability. Results show that language choice and use affect one's self-perceptions as a lecturer or academic. In many instances, language is perceived as an emotional obstacle, whether or not it is matched by an objective lack of linguistic competence. Positioning theory has been frequently used in the literature to investigate teacher identity, resulting in two contrasting stances: embracing the EMI identity or resisting it, usually through the use of multilingual practices. Further research is needed to evaluate the results and provide a synthesis of the included studies.Peer reviewe
The Cosmology attributed to Anania Širakac‘i : a revised critical edition, English translation, and a study of its sources and context
No full textThe object of the present dissertation is a treatise attributed to Anania Širakac‘i known as Tiezeragitut‘iwn, “Cosmology”. We propose a revised edition of this text, composed in Classical Armenian, its first complete English translation, and an analysis of medieval sources that offer a frame for its possible origin.
Part I focusses on Anania Širakac‘i as a historical figure and scholar and on the medieval sources concerning him and his activity. We argue that Širakac‘i was asked to produce a computus at the time of Catholicos Anastas, and discuss the possibility that the Cosmology was composed on the same occasion. Our analysis includes the question of Širakac‘i’s “k‘nnikon”, highlighting the strength and weaknesses of proposed interpretations of medieval sources depending on this term’s supposed meaning and use. We also devote a section to the influence that different cultural trends had on the representation of Širakac‘i, which, we argue, were in part derived from ideological interpretations of the Cosmology. Finally, we provide an overview of the major sources that this treatise draws from: works by St Basil of Caesarea, Aristotle and Philo of Alexandria. Parts II is devoted to the textual tradition of the Cosmology, presenting its printed editions and translations, the text’s recensions, a catalogue of manuscripts copies and an explanation of the work that was carried out for our revised edition. The latter constitutes part III, and it is preceded by a few premises and the siglae used for the manuscripts in the apparatus. Our English translation of this treatise is found in part IV, annotated with comments on contents, linguistic issues, translation choices, and parallels with other works, including sources. Part V presents some concluding remarks.
We also attach two appendices: Appendix I consists of a list of works attributed to Anania Širakac‘i; a tool to accompany the the reader through discussion on the corpus and potential relationships amongt texts. Appendix II contains an index of Biblical quotations and parallels identified in the Cosmology, including a comparison with the Hexaemeron of St Basil of Caesarea, via which most, but not all, citations came to be included in the Cosmology
Cthulhu : an open source molecular and atomic cross section computation code for substellar atmospheres
Get PDFFunding: RJM acknowledges support from NASA through the NASA Hubble Fellowship grant HSTHF2-51513.001 awarded by the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., for NASA, under contract NAS5- 26555.Atmospheric studies of exoplanets and brown dwarfs are a cutting-edge and rapidly evolving area of astrophysics research. Calculating models of exoplanet or brown dwarf spectra requires knowledge of the wavelength-dependent absorption of light (cross sections) by the molecules and atoms in the atmosphere. Here we introduce Cthulhu, a pure Python package that rapidly calculates cross sections from atomic and molecular line lists. Cthulhu includes modules to automatically download molecular line lists from online databases (e.g. ExoMol and HITRAN) and compute cross sections on a user-specified temperature, pressure, and wavenumber grid. Cthulhu requires only CPUs and can run on a user's laptop (for smaller line lists with < 100 million lines) or on a large cluster in parallel (for many billion lines). Cthulhu includes in-depth Jupyter tutorials in the online documentation. Finally, Cthulhu can be used as an educational tool to demystify the process of making cross sections for atmospheric models.Peer reviewe
Facing the ambiguities of participation in data-driven projects : a systematic literature review
Get PDFFunding: This research is part of the first author’s doctoral research, which is funded by a grant from the German Ministry of Education and Research (01IS20058) at the Alexander von Humboldt Institute for Internet and Society and a School of Computer Science Handsel Scholarship from the University of St Andrews.Participation is a prevalent topic in many areas, and data-driven projects are no exception. While the term generally has positive connotations, ambiguities in participatory approaches between facilitators and participants are often noted. How facilitators can handle these ambiguities, however, has been less studied. In this paper, we conduct a systematic literature review of participatory data-driven projects. We analyse 27 cases regarding their openness for participation and where participation most often occurs in the data lifecycle. From our analysis, we describe three typical project structures of participatory data-driven projects, combining a focus on labour and resource participation and/or rule- and decision-making participation with the general setup of the project as participatory-informed or participatory-at-core. From these combinations, different ambiguities arise. We discuss mitigations for these ambiguities through project policies and procedures for each type of project. Mitigating and clarifying ambiguities can support a more transparent and problem-oriented application of participatory processes in data-driven projects.Peer reviewe
Spectroscopic response of pH sensitive 5-hydroxy-5-methyl-3-[(4-phenlazo-phenylimino)-methyl]-benzaldehyde probe : a selective sensor towards acetate anion
Get PDFFunding: Authors extend their appreciation to Researchers Supporting number (RSPD2024R726) at King Saud University, Riyadh, Saudi Arabia for Funding this work.Sensing specific biological agents is important in terms of medicinal and pharmaceutical sectors. In this connection, development of point of care (POC) devices as per requirement with significant limit of detection (LOD) is of utmost importance. The present study reports the synthesis of a new class of sensing probe viz. 5-Hydroxy-5-methyl-3-[(4-phenlazo-phenylimino)-methyl]-benzaldehyde which bears a phenolic O–H group as the binding site and diazinyl functional group (Ph-N==N-Ph) as optical signalling moiety. Preliminary colorimetric studies establish that the presence of acetate anion (AcO−) in the solution causes a colour change from light yellow to red. NMR studies suggest probable binding mode of the reported probe is through the deprotonation of labile hydrogen of the phenolic OH-group, which in turn subsequently altered the optical properties of the probe. The sensing specificity of the reported probe is established through its photophysical characteristics. The binding constant magnitude of the probe using AcO− is calculated from fluorescence titration and determined to be 5.43× 106 M−1. This ascertains the strong binding ability of the probe with AcO− with an experimentally calculated limit of detection (LOD) to be ∼0.256 μM (15.11 ppb), as also substantiated through theoretical study. Such lower sensing level poses the present probe to be an effective anion sensor for acetate ion. The potential novelty lies in the detection of inorganic AcO− in aqueous analytical medium.Peer reviewe
Access Repository Dashboard
Do you manage St Andrews Research Repository? Access insider analytics, issue reports and manage access to outputs from your repository in the CORE Repository Dashboard!