32151 research outputs found
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Applying machine learning to predict reproductive condition in fish
Get PDFFunding: The present research was funded by grants for the fishing monitoring program and Common hake Acoustic Survey, projects conducted by the Instituto de Fomento Pesquero, IFOP-Chile. R. Wiff was funded by the Center of Applied Ecology and Sustainability (CAPES) project ANID PIA/BASAL FB0002 and by ANID-Programa Iniciativa Científica Milenio Código ICN2019-015.Knowledge of reproductive traits in exploited marine populations is crucial for their management and conservation. The maturity status in fish is usually assigned by traditional methods such as macroscopy and histology. Macroscopic analysis is the assessing of maturity stages by naked eye and usually introduces large amount of error. In contrast, histology is the most accurate method for maturity staging but is expensive and unavailable for many stocks worldwide. Here, we use the Random Forest (RF) machine learning method for classification of reproductive condition in fish, using the extensive data from Chilean hake (Merluccius gayi gayi). Gonads randomly collected from commercial industrial and acoustic surveys were classified as immature, mature-active and mature-inactive. A classifier for these three maturity classes was fitted using RFs, with the continuous covariates total length (TL), gonadosomatic index (GSI), condition factor (Krel), latitude, longitude, and depth, along with month as a factor variable. The RF model showed high accuracy (>82%) and high proportion of agreement (>71%) compared to histology, with an OOB error rate lower than 15%. GSI and TL were the most important variables for predicting the reproductive condition in Chilean hake, and to lesser extent, depth when using survey data. The application of the RF shows a promising tool for assigning maturity stages in fishes when covariates are available, and also to improve the accuracy of maturity classification when only macroscopic staging is available.Peer reviewe
New directions for leader personality research : breaking bad in foreign policy
Get PDFThis article considers how leaders' personality traits change over time. I focus on how leaders become more authoritarian, overconfident and more mistake-prone; how, when and why do leaders 'break bad'? Temporal evolution of leaders is an important topic given the long tenure of many political leaders and the influence these leaders have over policies, including foreign policies. There is very little work on how leaders' personalities develop and how they interact with changing constraints and opportunities. This article is an agenda-setting review, designed to push foreign policy analysis in new directions. This is especially important given the resurgence in research on personalities and the renewed interest in leaders. Drawing on diverse and multi-disciplinary scholarship on the psychological effects of aging, experience, learning and power-holding, this article develops expectations about leader personality change. I discuss challenges for research in this area, focusing on how 'bad' can be conceptualized, and offer specific avenues for future investigations.Peer reviewe
Tracking developmental differences in real-world social attention across adolescence, young adulthood and older adulthood
Get PDFFunding: This work was carried out with the support of a European Research Council grant to H.J.F. (CogSoCoAGE; 636458).Detecting and responding appropriately to social information in one’s environment is a vital part of everyday social interactions. Here, we report two preregistered experiments that examine how social attention develops across the lifespan, comparing adolescents (10–19 years old), young (20–40 years old) and older (60–80 years old) adults. In two real-world tasks, participants were immersed in different social interaction situations—a face-to-face conversation and navigating an environment—and their attention to social and non-social content was recorded using eye-tracking glasses. The results revealed that, compared with young adults, adolescents and older adults attended less to social information (that is, the face) during face-to-face conversation, and to people when navigating the real world. Thus, we provide evidence that real-world social attention undergoes age-related change, and these developmental differences might be a key mechanism that influences theory of mind among adolescents and older adults, with potential implications for predicting successful social interactions in daily life.Peer reviewe
The academic staff community of St Andrews, 1700-1900 : methods and definitions
Get PDFFunding: St Andrews and the Legacies of Empire fellowship.This working paper explains the ‘Methods’ and ‘Definitions’ of the research underpinning ‘Section 4: the Academic Community’ and ‘Section 5: Ideas & Inquiry’ of the final report on St Andrews and the Legacies of Empire (2024). The text below was composed as the opening sections of a report on ‘The Academic Staff Community of St Andrews, 1700-1900’ presented to the Legacies of Empire steering group in March 2023 (which was itself an update on an internal report from August 2022). See also Working Paper C, on ‘Chancellors and the Legacies of Empire’ (March 2023)
A new data-driven paradigm for the study of avian migratory navigation
Get PDFAvian navigation has fascinated researchers for many years. Yet, despite a vast amount of literature on the topic it remains a mystery how birds are able to find their way across long distances while relying only on cues available locally and reacting to those cues on the fly. Navigation is multi-modal, in that birds may use different cues at different times as a response to environmental conditions they find themselves in. It also operates at different spatial and temporal scales, where different strategies may be used at different parts of the journey. This multi-modal and multi-scale nature of navigation has however been challenging to study, since it would require long-term tracking data along with contemporaneous and co-located information on environmental cues. In this paper we propose a new alternative data-driven paradigm to the study of avian navigation. That is, instead of taking a traditional theory-based approach based on posing a research question and then collecting data to study navigation, we propose a data-driven approach, where large amounts of data, not purposedly collected for a specific question, are analysed to identify as-yet-unknown patterns in behaviour. Current technological developments have led to large data collections of both animal tracking data and environmental data, which are openly available to scientists. These open data, combined with a data-driven exploratory approach using data mining, machine learning and artificial intelligence methods, can support identification of unexpected patterns during migration, and lead to a better understanding of multi-modal navigational decision-making across different spatial and temporal scales.Peer reviewe
Transcultural adaptation and evaluation of the psychometric properties of the Spanish version of the FCR7 questionnaire for assessing fear of recurrence in cancer patients: FCR6/7-SP
Get PDFBackground/Objectives: Fear of recurrence is one of the main issues affecting cancer patients after the completion of treatment. Despite the development of various assessment tools at the international level, there is a lack of validated questionnaires in Spanish. For this reason, the aim of this study is to conduct a transcultural adaptation and evaluate the psychometric properties of the Spanish version of the Fear of Cancer Recurrence (FCR7) questionnaire. Methods: We carried out translation and transcultural adaptation of the FCR7 scale, content validity through expert review, and face validity with a pilot test in the first phase. In the second phase, construct validity was evaluated through confirmatory factor analysis and Rasch analysis, along with reliability (internal consistency), convergent–divergent validation, and known-groups validation in a sample of 315 individuals with a history of cancer. Descriptive and inferential analysis was performed using JAMOVI© v.2.3.24., confirmatory factor analysis with FACTOR© v.12.02.01x64 bits, and Rasch analysis with JMetrik© v.2.0. Results: Aiken’s coefficient exceeded 0.75 for all items, indicating acceptable face validity for the instrument. Two unidimensional models were obtained for the instrument, FCR7-SP and FCR6-SP, both showing acceptable fit values and adequate reliability (omega coefficient = 0.933 [95% CI: 0.922–0.944] and 0.942 [95% CI: 0.931–0.951], respectively). Conclusions: The Spanish version of the FCR7 is valid and reliable for assessing fear of cancer recurrence in the Spanish population, with two models available for its application (FCR7-SP and FCR6-SP). The availability of this tool will enable the evaluation of this phenomenon in clinical practice and a more effective approach to addressing its consequences.Peer reviewe
PathoGD : an integrative genomics approach to primer and guide RNA design for CRISPR-based diagnostics
Get PDFFunding: This study was funded by the Victorian Medical Research Accelerator Fund (GA-F3791196–5514) and the Australian Government Department of Health (PO4932). D.A.W. is supported by an NHMRC Investigator Grant (APP1174555). This work was also supported by an Australian Research Council Industrial Transformation Research Hub Grant (IH190100021).Critical to the success of CRISPR-based diagnostic assays is the selection of a diagnostic target highly specific to the organism of interest, a process often requiring iterative cycles of manual selection, optimisation, and redesign. Here we present PathoGD, a bioinformatic pipeline for rapid and high-throughput design of RPA primers and gRNAs for CRISPR-Cas12a-based pathogen detection. PathoGD is fully automated, leverages publicly available sequences and is scalable to large datasets, allowing rapid continuous monitoring and validation of primer/gRNA sets to ensure ongoing assay relevance. We designed primers and gRNAs for five clinically relevant bacterial pathogens, and experimentally validated a subset of the designs for detecting Streptococcus pyogenes and/or Neisseria gonorrhoeae in assays with and without pre-amplification. We demonstrated high specificity of primers and gRNAs designed, with minimal off-target signal observed for all combinations. We anticipate PathoGD will be an important resource for assay design for current and emerging pathogens. PathoGD is available on GitHub at https://github.com/sjlow23/pathogd .Peer reviewe
Improving biodiversity resilience requires both public and private finance : a life-cycle analysis of biodiversity finance
Get PDFFunding: Jesper Beverdam wants to thank the Ubbo Emmius Foundation (UEF) at the University of Groningen for funding his PhD research for the project 'Innovative financial instruments for sustainable landscapes' via their M20 grant scheme.There is a substantial ‘biodiversity financing gap’: each year, only about one sixth of the funding required for biodiversity conservation is actually provided. Most biodiversity financing is from public sources; less than one fifth is from private ones. However, the potential of private financing is huge and could help fill the biodiversity financing gap. We study how this might be achieved by using a life cycle analysis for biodiversity, identifying the various phases a stylized biodiversity restoration- or conservation project passes through. Public funding offers most potential in the early stages of a biodiversity project, when financing requirements are relatively low, but uncertainty is high. Private and blended finance demonstrate potential in later stages, when financing requirements are higher, but uncertainty is lower and return mechanisms have been established. We contribute theoretically by proposing a novel framework through which the financing options of biodiversity interventions can be considered. Practically, the framework assists in advancing the understanding of the field of funding possibilities for entities wishing to develop projects with the aim of conserving and/or restoring biodiversity.Peer reviewe
Pharmacological characterisation of a clinical candidate, TG-0054, a small molecule inverse agonist targeting CXCR4
No full textFunding: This research was funded by a European Union’s Horizon2020 MSCA Program (Grant agreement 860229 [ONCORNET2.0]), and C.P. was funded under the same program [Grant agreement 101063969]. Finally, N.B. and S.M. were funded by the Netherlands Organization for Scientific Research (NWO) [Grant agreement 881 ENPPS.TA.019.003].CXCR4 is an important therapeutic target for hematopoietic stem cell mobilization, which enhances the success of autologous stem cell transplantation for treating blood cancers such as lymphomas and myeloma. As CXCR4 has been shown to be involved in various inflammatory diseases, cancer progression, and cell entry by the human immunodeficiency virus, understanding the molecular mechanism of CXCR4 inhibitors has potential implications in a wide area of diseases. Here, we present an exploratory study which involves the molecular pharmacological characterization of TG-0054 (burixafor, GPC-100), a clinical candidate for hematopoietic stem cell mobilization. TG-0054 inhibited CXCL12 binding at CXCR4, and antagonized both Gαi and β-arrestin2 recruitment as well as the downstream Gαi-attenuation of cAMP signaling pathway, with pIC50 of 7.7, 8.0, and 7.9, respectively. Compared with the clinically used antagonist AMD3100 and the prototypical inverse agonist Isothiourea-1t (IT1t), TG-0054 displayed a unique pharmacological profile. Like IT1t, TG-0054 inhibited the constitutive Gαi signaling of CXCR4. However, in contrast to IT1t and other reported inverse agonists, TG-0054 was not able to induce monomerization of CXCR4 oligomeric complexes. Considering the unique properties of TG-0054 on CXCR4, TG-0054 is an interesting tool compound for studying the relevance of inverse agonism as well as CXCR4 monomerization in various pathologies.Peer reviewe
The ubiquitylation of IL-1β limits its cleavage by caspase-1 and targets it for proteasomal degradation
Get PDFFunding: We gratefully acknowledge grant support from the National Health and Medical Research Council (NHMRC) of Australia: project grants (1145788 to J.E.V., K.E.L. and J. M.M.; 1101405 to J.E.V.; 1162765 to K.E.L.), Ideas grants (1183070 to J.E.V.; 1181089 to K.E.L.) and fellowships (1172929 to J.M.M.; 1141466 to J.E.V.). K.E.L. is an Australian Research Council (ARC) Future Fellow (FT190100266). J.S.P. is supported by an Australian NHMRC Career Development Fellowship (1159230). MJH is and NHMRC Senior Research Fellow (1156095) and supported by the Leukemia and Lymphoma Society SCOR grant 7015–18. The generation of the Il1b K133R/K133R mice used in this study was supported by the Phenomics Australia (PA) and the Australian Government through the National Collaborative Research Infrastructure Strategy (NCRIS) program. This work was also supported by operational infrastructure grants through the Australian Government Independent Research Institute Infrastructure Support Scheme (9000653) and the Victorian State Government Operational Infrastructure Support, Australia.Interleukin-1β (IL-1β) is activated by inflammasome-associated caspase-1 in rare autoinflammatory conditions and in a variety of other inflammatory diseases. Therefore, IL-1β activity must be fine-tuned to enable anti-microbial responses whilst limiting collateral damage. Here, we show that precursor IL-1β is rapidly turned over by the proteasome and this correlates with its decoration by K11-linked, K63-linked and K48-linked ubiquitin chains. The ubiquitylation of IL-1β is not just a degradation signal triggered by inflammasome priming and activating stimuli, but also limits IL-1β cleavage by caspase-1. IL-1β K133 is modified by ubiquitin and forms a salt bridge with IL-1β D129. Loss of IL-1β K133 ubiquitylation, or disruption of the K133:D129 electrostatic interaction, stabilizes IL-1β. Accordingly, Il1bK133R/K133R mice have increased levels of precursor IL-1β upon inflammasome priming and increased production of bioactive IL-1β, both in vitro and in response to LPS injection. These findings identify mechanisms that can limit IL-1β activity and safeguard against damaging inflammation.Peer reviewe
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