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Relaxation of natural selection in the evolution of the giant lungfish genomes
Get PDFFunding: This work was supported by the University of Ferrara (Italy) and funded by the MIUR PRIN 2017 grant 201794ZXTL to G.B. S.F., G.B., and R.B. are deeply grateful to Jane Hughes and Dan Schmidt for their hospitality at the Griffith University, Queensland, and for their friendship.Nonadaptive hypotheses on the evolution of eukaryotic genome size predict an expansion when the process of purifying selection becomes weak. Accordingly, species with huge genomes, such as lungfish, are expected to show a genome-wide relaxation signature of selection compared with other organisms. However, few studies have empirically tested this prediction using genomic data in a comparative framework. Here, we show that 1) the newly assembled transcriptome of the Australian lungfish, Neoceratodus forsteri, is characterized by an excess of pervasive transcription, or transcriptional leakage, possibly due to suboptimal transcriptional control, and 2) a significant relaxation signature in coding genes in lungfish species compared with other vertebrates. Based on these observations, we propose that the largest known animal genomes evolved in a nearly neutral scenario where genome expansion is less efficiently constrained.Peer reviewe
Numidia and Rome
Get PDFThis article explores issues and possibilities in the study of Numidia and Rome. It considers the history of scholarship, new methodologies, and several representative examples. Particular attention is given to Latin literary and cultural representation of ancient Numidia with an eye on how Numidian perspectives can also enter the conversation, despite major gaps in the archive.Peer reviewe
Exploring the landscape of EFL teachers' professional development in China : a scoping review
Get PDFWhile Continuous Professional Development (CPD) for all teachers is a key attribute of China’s educational landscape, there are few studies that have been published in English on in-service English-as-a-Foreign-Language (EFL) teacher support in its elementary and secondary schools. This is the first scoping review of English-language research into in-service Chinese teachers’ CPD, which aims to explore what has been published over the past 15 years in order to gain a better understanding of this vast, dynamic, and often misunderstood context. Following a rigorous and systematic methodological framework, we identified 27 recently published articles and book chapters, focusing on their bibliographic characteristics while considering how these individual studies might be unified, ultimately contributing to a more holistic understanding of CPD provision for in-service Chinese EFL teachers. We conclude with recommendations for CPD providers, for policy-makers, and for future researchers to use this study as a step towards further exploration into this unique context.Peer reviewe
SurGen: 1020 H&E-stained whole slide images with survival and genetic markers
Get PDFFunding: C.M. is supported by NHS Lothian. This work is supported in part by the Industrial Centre for AI Research in Digital Diagnostics (iCAIRD), which is funded by Innovate UK on behalf of UK Research and Innovation (UKRI) (project number 104690).Background: Cancer remains one of the leading causes of morbidity and mortality worldwide. Comprehensive datasets that combine histopathological images with genetic and survival data across various tumour sites are essential for advancing computational pathology and personalised medicine. Results: We present SurGen, a dataset comprising 1,020 H&E-stained whole-slide images (WSIs) from 843 colorectal cancer cases. The dataset includes detailed annotations for key genetic mutations (KRAS, NRAS, BRAF) and mismatch repair status, as well as survival data for 426 cases. We illustrate SurGen’s utility with a proof-of-concept model that predicts mismatch repair status directly from WSIs, achieving a test area under the receiver operating characteristic curve of 0.8273. These preliminary results underscore the dataset’s potential to facilitate research in biomarker discovery, prognostic modelling, and advanced machine learning applications in colorectal cancer and beyond. Conclusions: SurGen offers a valuable resource for the scientific community, enabling studies that require high-quality WSIs linked with comprehensive clinical and genetic information on colorectal cancer. Our initial findings affirm the dataset’s capacity to advance diagnostic precision and foster the development of personalised treatment strategies in colorectal oncology.Peer reviewe
Two pre-theoretic counterexamples to justification holism in the epistemology of logic
Get PDFAn abductivist approach to the epistemology of logic has recently gained traction. A necessary component of logical abductivism is justification holism, asserting that claims of logical entailment can be justified only in the context of an entire logical theory, for example, classical, intuitionistic, and so on. One view that is incompatible with abductivism is an atomistic view on which individual entailment claims can be justified pointwise rather than in the context of a whole theory. This paper provides two atomistic counterexamples to justification holism in the epistemology of logic. Both examples appeal to pre-theoretic commitments of deductive validity. The main aim is to show that there are some foundational entailment claims for which we can have propositional justification independently of theory choice and outside the context of a whole logical theory. If one were to give up on these foundational claims, all semantic and syntactic accounts of deductive validity would be non-starters.Peer reviewe
Making everyday life : amateur photography and print media in China, ca. 1920-1937
No full textThis thesis explores how amateur photography and print media in China between 1920 and 1937 intersected to create a new genre of everyday life photography. A close examination of this largely overlooked category offers a new lens to understand transformations in both the history of photography and the social history of early twentieth-century China. It asks how photography became an everyday social practice among middle- and upper-class urbanites, and how everyday life emerged as a central subject for these amateur photographers. I investigate the role of the Western company Kodak in Shanghai alongside the rapid modernisation of Chinese society, which facilitated photography’s integration into family life, education and travel experiences.
This study adopts a critical approach to examine the crucial role of print media and the contextual significance of the public presentation of everyday life photographs in newspapers, magazines and graduation annuals. It emphasises how photography and print media together shaped the conception, representations and social conventions of “everyday life”. My critical analyses of published everyday life photographs reveal how young, modern Chinese men and women used, perceived and engaged with photography and print media to represent, express and aspire to their self-identities, social class, gendered roles, community belonging and national sentiment. This thesis underscores the significance of everyday life photographs — so often regarded as merely ordinary and light-hearted — by uncovering their nuanced cultural and social attributes in the making of everyday life in early twentieth-century China."I am grateful to the Elizabeth Gilmore Holt Travel Scholarship, the St Leonard’s College Travel Fund, and the British Postgraduate Network for Chinese Studies Postgraduate Research Grant for their financial support, which facilitated my archival research and access to primary sources. This thesis is supported by the China Scholarship Council-St Andrews Joint Scholarship."--Fundin
A functional limit theorem for a dynamical system with an observable maximised on a Cantor set
Get PDFWe consider heavy-tailed observables maximised on a dynamically defined Cantor set and prove convergence of the associated point processes as well as functional limit theorems. The Cantor structure, and its connection to the dynamics, causes clustering of large observations: this is captured in the ‘decorations’ on our point processes and functional limits, an application of the theory developed in a paper by the latter three authors.Peer reviewe
Not by selection alone : expanding the scope of gene-culture coevolution
Get PDFGene-culture coevolution (GCC)—an ambitious synthesis of biological and social sciences is often used to explain the evolution of key human traits. Despite the framework's broad conceptual appeal however, empirical evidence is often perceived as limited to a few key examples like lactase persistence. We argue this apparent gap between theoretical appeal and empirical evidence stems from conceptual ambiguities regarding the scope of relevant gene-culture interactions. Drawing on recent work in animal gene-culture coevolution and human genomics, we propose a “broad” approach that formally incorporates drift and migration alongside natural selection. This builds upon and subsumes the existing “narrow” framework focused on selection. Through case studies of skin pigmentation evolution and gift-exchange network influences on genetic variation in Melanesia, we demonstrate how cultural factors shape both adaptive and neutral genetic variation and population structure. This integrative perspective accommodates diverse empirical findings while opening new avenues for research in human evolution.Peer reviewe
“You’re not informed unless you make it your business” : insights from a Scottish national study exploring attitudes towards residential rehabilitation
Get PDFFunding: The original study was funded by Public Health Scotland [PHS2022-23C009].Background Despite Scotland’s commitment to patient-centred substance use care, little is known about how individuals learn of residential rehabilitation. This study explores whether national policy goals of informed decision-making translate into on-the-ground practice. Methods This paper presents a secondary analysis of data generated during a larger mixed-methods evaluation of residential rehabilitation. Participants (n = 197 people who reported a drug problem in the previous 12 months) were recruited from 29 Scottish Local Authority areas and completed structured face-to-face interviews. Peer researchers with lived experience conducted interviews. Qualitative data were thematically examined according to macro-level (systemic), meso-level (community), and micro-level (individual) influences. Results Many participants reported never being informed of residential rehabilitation by healthcare providers. In response, peers, family, and community support groups filled information gaps, though their accounts were inconsistent or contradictory. Consequently, individuals resorted to micro-level strategies, such as internet searches and repeated questioning of key workers, to piece together essential details. Participants frequently expressed frustration with missed opportunities to explore alternative treatment pathways, compounding a sense of systemic neglect and disempowerment. This dynamic interplay between macro, meso, and micro factors often hindered genuinely informed decision-making and undermined policy ambitions for accessible, rights-based care. Conclusions Findings highlight pervasive communication gaps, echoing other contexts where new or less-familiar treatment options remain poorly signposted. Mandated communication protocols, formal peer collaboration, and reduced burdens on individuals could strengthen the alignment between practice and Scotland’s National Mission. By closing these knowledge gaps, services can better support people with problem substance use to make truly informed decisions about residential rehabilitation and broader treatment pathways.Peer reviewe
Mapping a Chinese plan for the Kowloon walled city : an initial documentary and topographical interpretation
Get PDFThis short paper on the planning and development of the City of Kowloon (City) at its formative (pre-British colonial) stage as a walled Ch’ing (Qing) Dynasty military base, attempts to provide a reasonable account of the apparent in-completion of this imperially planned town. The account is based on a comparison of the written specifications of this City’s design in written narratives in Chinese official documents, and its actual physical configuration after 1847 as it appears in photos, maps, and written sources. The authors postulate that the abandonment of the originally-proposed dimensions, a “Chun Hoi Lau” (Zhenhai Tower) which venerated the god Pak Tei (Beitei) with a strong fung shui (feng shui) function, and an uphill gun (cannon) position, was due to local objective topographical and geotechnical constraints that were insurmountable given China’s perceived urgent military needs at the time.Peer reviewe
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