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Genome assemblies of Nuttall’s White-crowned sparrow (Zonotrichia leucophrys nuttalli) and Rufous-collared sparrow (Zonotrichia capensis)
No full textThe Zonotrichia sparrows, belonging to the Passerellidae family, are widely studied for their vocalizations and genetic diversity. Here, we present two high-quality genome assemblies for Zonotrichia species; the northern hemisphere Nuttall's white-crowned sparrow (Zonotrichia leucophrys nuttalli, NWCS) and the southern hemisphere rufous-collared sparrow (Zonotrichia capensis chilensis, RUFS). These assemblies were assembled using PacBio long-reads and Omni-C chromatin conformation technology, integrated with RNA-sequencing data to provide genome annotations. The NWCS assembly comprises 1.12 Gb anchored to 30 chromosomes, while the RUFS assembly includes 1.11 Gb on 27 chromosomes. Both assemblies exhibit high completeness and contiguity, with 96.6% and 96.9% complete BUSCOs (Benchmarking Universal Single-Copy Orthologs) for NWCS and RUFS, respectively. These genome assemblies provide valuable resources for future research on genetic divergence, vocal learning, evolution and responses to climate change within the Zonotrichia genus.</p
Fairness by design:Cross-cultural perspectives from children on AI and fair data processing in their education futures
No full textAI-driven educational technologies (AI-EdTech) process extensive data, raising concerns about commercial exploitation of children’s data and risks to their privacy, wellbeing, agency, and legal rights. The ‘fairness principle’ in data protection law requires fair data processing that meets children’s expectations and avoids unexpected, detrimental, discriminatory, or misleading practices. However, children’s own perspectives on what fairness means in AI-EdTech are underexplored in design. This study bridges the gap between law and design research to contextualize what fairness means through co-design workshops with 72 children (aged 10–12) and 4 teachers (N=76) in Scotland and Türkiye. We examine how children’s perspectives can inform the operationalization of ‘fairness by design’ for AI-EdTech. Our contributions include: (1) an understanding of children’s perspectives on how fairness manifests (or does not) in AI-EdTech and (2) recommendations for both design and legal communities to align AI-EdTech design and data practices with children’s values and rights
Shortening duration of untreated illness in young people with first episode eating disorders:Protocol of a randomised controlled feasibility trial of a smartphone friendly multi-modal decision-making tool (FREED-M) to improve help-seeking
No full textBackground: Early intervention gives young people the best chance to recover from eating disorders (EDs). An important focus of early intervention is shortening the time between a person first developing symptoms and starting treatment (duration of untreated eating disorder; DUED). Patient-related factors (e.g. poor mental health literacy and help-seeking difficulties) are strongly associated with DUED. The aims of our study are to co-design and test the feasibility of FREED-Mobile (FREED-M), an online intervention tool for young people with early-stage EDs. This tool aims to improve knowledge about EDs, increase motivation to seek treatment and teach early steps towards change or recovery, thus reducing DUED. Methods: We will carry out a randomised controlled feasibility trial comparing the FREED-M tool with a control intervention where individuals are sign-posted to an ED charity website. The objectives of the proposed trial are to establish/estimate: (a) attrition rates at follow-up (primary feasibility outcome); (b) participant recruitment; (c) intervention uptake, completion rates and acceptability; (d) intervention effect sizes and standard deviations for outcomes to inform the sample size calculation for a large-scale randomised controlled trial (RCT); (e) stakeholder views on the intervention. We aim to recruit 116 participants (young people, aged 16–25, with first episode ED) from primary care, schools and universities, ED services and social media. Online assessments will be carried out at baseline, end of intervention and follow-up (weeks 0, 4 and 12 post-randomisation, respectively). Outcomes will include motivation and readiness to change, attitudes and intentions towards help-seeking, ED symptoms, mood and social functioning, and health-related quality of life. Additionally, we will carry out a qualitative evaluation of participants’ views of the intervention and study design. Discussion: The results of this feasibility trial will inform adaptations to the intervention as needed, as well as the study design (e.g. sample size, primary outcomes) of a future large-scale RCT to assess the effectiveness of the FREED-M intervention. If effective, this novel, online intervention has the potential for wide dissemination and for substantially reducing DUED to improve long-term patient outcomes. Trial registration: ISRCTN, ISRCTN15662055. Registered 27 July 2022, https://www.isrctn.com/ISRCTN15662055
Bridging the gap:How transport infrastructure reduces bilateral trade costs to fuel GDP growth
Get PDFAlthough scholars generally recognize infrastructure development as a pivotal pillar for economic progress, a gap remains in the current literature regarding how transport infrastructure affects GDP growth. This study examines how transport infrastructure impacts GDP growth by reducing trade costs. It confirms that improving the quality of transport infrastructure lowers these costs. Specifically, a 1% improvement in the average transport infrastructure quality between an emerging and a developed economy can reduce bilateral trade costs by up to 0.71%. To estimate the net effect of changes in infrastructure on GDP growth via trade costs, we used the Computational General Equilibrium framework. The results demonstrate significant potential for enhancing GDP growth across different groups of countries based on their level of economic development (i.e. developing countries, emerging countries, and developed countries). The broader implications of transport infrastructure development for the global economy are also examined
Mitogenomic analysis of Thai Sunda pangolins reveals regional phylogeography, and informs conservation management
Get PDFPangolins are considered the most trafficked mammals in the world with all eight species listed on CITES Appendix I. Despite this pervasive threat to their survival, there remains a limited understanding of genetic diversity and connectivity among populations of Asian pangolin species, hampering effective conservation management. We analysed mitogenome sequences of the Sunda pangolin (Manis javanica) from across their Southeast Asia continental distribution, as well as Borneo. Phylogenetic reconstruction revealed six lineages, with clear separation north and south of the Kangar-Pattani biogeographic line in southern Thailand, revealing clear differentiation between Sundaland and Indochinese Sunda pangolin lineages. Further divergence across an east-west divide was observed in central and northern Thailand, extending northwards towards China. Our results provide new insights into the evolutionary relationships among Sunda pangolin populations in Southeast Asia, building on other recent research in this field and helping to establish the species’ baseline phylogeography. These inferences will aid conservation planning and support the genetic traceability of the illegal pangolin trade
The Effect of core filling on seismic performance of pretensioned centrifugal spun concrete piles with steel strands
Get PDFPretensioned centrifugal spun concrete piles with steel strands have been developed to improve the seismic performance of precast-prestressed concrete hollow piles. In this paper, two pile specimens with reinforced concrete infilling were fabricated, and lateral cyclic loading tests were conducted. A finite element model is developed to predict the hysteretic characteristics of core-filled pile specimens. The results show that reinforced concrete infilling improves the cracking pattern and failure mode of piles. Core-filled piles exhibit better structural stability and higher deformability than hollow piles. Reinforced concrete infilling enhances the lateral load-carrying capacity and deformability more significantly than plain concrete infilling
A systematic review of interventions with families of trans people
Get PDFIntroductionTrans people experience poorer mental health than their cisgender counterparts, likely as a result of minority stress. Caregivers can contribute to minority stress through discrimination, rejection and lack of acceptance. Interventions with family members may provide a way to address conflict and lack of acceptance of gender within the family.MethodA systematic review was conducted following PRISMA guidelines. Searches were conducted in PsycInfo, Embase, MEDLINE, Cinahl Plus and ProQuest Theses and Dissertations databases on 16 February 2024 to identify concepts relating to “transgender” and “family intervention.”ResultsSeven studies were included in the review. Four evaluated interventions relating to family therapy, two to caregiver support groups, and one to an online psychoeducational programme. Outcomes related to mental health were reported on most commonly with positive results; however, overall study quality was poor, and study designs varied.DiscussionMore studies on the efficacy of family-based interventions with trans people have been published in recent years. Due to heterogeneity, the conclusions that can be drawn from this review are limited. Recommendations are made for increasing the quality of future studies. The recent increase in studies assessing family interventions with trans people is an encouraging sign, and several interventions were identified that show promise in the ways they have adapted for the needs of trans people
Age-related impairment of intestinal inflammation resolution through an eicosanoid-immune-microbiota axis
Get PDFAging manifests a decline of immune function, induces microbiome dysbiosis, drives organ inflammation, and impedes the resolution of inflammation. However, the mechanisms underlying age-related intestinal inflammation remain poorly described. Here we find that the resolution of T cell-initiated intestinal inflammation is impaired with aging. This impairment is mediated by disrupting the immune-microbiota interplay, controlled by intestinal eicosanoid metabolism. Pharmacologically inhibiting eicosanoid biosynthesis, blocking the prostaglandin E receptor subtype 4 (EP4), or genetically ablating EP4 diminishes age-related impairment of intestinal inflammation resolution. Mechanistically, mononuclear phagocyte-intrinsic eicosanoid-EP4 signaling impedes the resolution of intestinal inflammation, through fostering gut microbial dysbiosis and, more importantly, interrupting segmented filamentous bacteria adhesion to the intestinal epithelium. Colonization with EP4-ablated mouse microbiota or segmented filamentous bacteria improves the resolution of intestinal inflammation. These findings reveal that eicosanoid-dependent immune-microbiota interactions impair inflammation resolution in the aged intestine, highlighting potential intervention strategies for improving age-related gut health
Fully Phased Population-Prevalent East African Cattle BoLA-I Alleles Determined Using PacBio HiFi Long-Read Sequencing Represent Five Novel Specificities With Distinctive Peptide Binding Potential
No full textDue to factors such as lower biosecurity, greater wildlife/farm animal interfaces, and environmental challenges, cattle in sub-Saharan Africa are exposed to more diverse and intensive bacterial, viral and protozoan pathogen challenges than cattle in Europe and other high-income regions of the world. Classical class I genes of the major histocompatibility complex (MHC) contribute to protection from diseases caused by these pathogens by refining a huge pool of potential pathogen-derived peptide ligands into a smaller ensemble for presentation to CD8+ T cells. Knowledge of population-prevalent MHC alleles is therefore critical for evidence-based approaches to vaccine design and improved understanding of pathogen resistance. Whereas variation in MHC molecules is understood in most detail for European Bos taurus, the alleles expressed by Africa's cattle remain poorly defined. We have leveraged recent improvements in the accuracy of PacBio high-fidelity (HiFi) circular consensus sequencing (CCS) and adapted stringent sequence filtering algorithms to identify hundreds of as yet uncharacterised fully phased BoLA-I alleles from multiple populations of African taurine (Ankole) and indicine (Zebu) cattle in East Africa. The analysis highlights a convergence of population-prevalent class I MHC allelic repertoires in taurine and indicine cattle, likely due to the similar pathogen-driven selective pressures. Our analysis of the anchor residue accommodating pockets of these prevalent alleles revealed extremely high levels of polymorphism, which contrast with Holstein alleles that exhibit a more limited repertoire of MHC specificity-determining pocket residues, potentially constraining the breadth of peptide presentation. However, in the context of considerable sequence and physicochemical variation in the pocket-forming residues, it was possible to discern overlaps in the predicted peptide binding spectrum. Interrogation of potential differences in peptide binding specificities with European B. taurus alleles revealed that the fully phased African cattle class I MHC alleles represent five novel specificities. We envisage that this novel finding will find broad application in assessing potentially achievable vaccination coverages of future pathogen-encoded vaccine candidates against important intracellular pathogens. One aim of future research should be to leverage recent improvements in the sensitivity of mass spectrometry combined with immunoprecipitation of peptides bound to African cattle MHC to search directly for T-cell epitopes in the context of the inferred 'supertype' diversity.</p
Pre-sleep screen time and screen time addiction as shared determinants of poor sleep and obesity in adolescents aged 11-14 years in Scotland
No full textBackground: The overall quantity of screen time has been associated with short sleep duration and increasingly sedentary lifestyles, leading to adiposity. The aim of this research was to explore which components of screen time usage are shared determinants of poor sleep and higher adiposity in adolescents, using data from the Teen Sleep Well Study.Methods: A cross-sectional study of adolescents aged 11-14-years in Fife, Scotland was conducted. Sleep was measured objectively using the Actigraph GT3X-BT and subjectively using validated questionnaires. Adiposity was assessed using body fat percentage (BF%) and obesity was measured using body mass index percentile (BMIp). Four components of screen time were addressed using questionnaires: the timing of screen time, quantity of screen time, location of screen time, and screen time addiction. Descriptive statistics and statistical tests such as Pearson correlation tables, and adjusted regression analyses were used. Mediation analyses explored wellbeing as a factor in the association between screen time and sleep and obesity. Results: 62 participants (33 Female/29 Male, mean age 12.2±1.1 years, mean BMIp 60.3±32.1) completed the study. Excessive screen time pre-sleep (30 minutes before sleep) and post-sleep (first 30 minutes after waking), excessive screen time on a weekend, and screen time addiction were shared determinants of higher adiposity, a later chronotype (evening-preference) and poor sleep outcomes: poor sleep habits, increased insomnia symptoms (IS) and increased sleep onset variability. Mediation analyses confirmed that adolescent wellbeing mediated the association between pre-sleep screen time and IS (36.3%) and BF% (21.9%), post-sleep screen time and IS (37.7%) and BF% (30.4%), videogaming addiction and IS (31.9%) and BF% (34.6%), social media addiction and IS (35.0%) and BF% (17.4%), mobile phone addiction and IS (34.0%) and BF% (10.6%), weekday screen time and IS (58.1%) and BF% (39.8%), and weekend screen time and IS (51.4%) and BF% (38.0%).Conclusions: These screen time behaviours, alongside wellbeing should be considered in multi-component health-promoting interventions aimed at improving adolescent sleep and reducing obesity risk. Future research should employ longitudinal designs to clarify the directionality of these associations and determine the effectiveness of interventions that target both screen time behaviours and wellbeing
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