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<p>This report describes features of actinobacteriophages assigned to subcluster AZ1. &nbsp;Additional phages may have been added to the phagesDB database since the generation of this report.</p>
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Abstract Description The identification and prioritization of cancer-specific neoepitopes from next-generation sequencing data for personalized immunotherapies such as cancer vaccines remains challenging and requires the use of complex bioinformatics approaches. Here, we present GeNeo2, an updated version with enhanced features of the GeNeo toolbox for predicting neoepitopes from matched tumor/normal exome sequencing data coupled with tumor RNA-Seq data (Al Seesi et al., 2023). Unlike GeNeo, which identifies neoepitopes generated by single nucleotide variants, GeNeo2 also predicts neoepitopes generated by somatic indels. A distinguishing feature in GeNeo2 is that it integrates tools for analyzing mass spectrometry immunepeptidomic data, which can reveal neoantigens derived from both canonical and noncanonical sources. Finally, GeNeo2 integrates novel machine-learning approaches to improve the accuracy of somatic variant calling and peptide identification from mass spectrometry data. GeNeo2 tools can be accessed via web-based interfaces deployed on a Galaxy portal accessible at https://neo.engr.uconn.edu/. A virtual machine image for running GeNeo2 locally is also available to academic users upon request. Topic Categories Computational and Systems Immunology (COMP)
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This article explores a collaborative initiative undertaken by a state university aimed at implementing and expanding an Early College Program. The conceptual framework, practical strategies, collaborative efforts and background of this initiative are presented. With a focus on improving college access for all, the article introduces the university's efforts to promote an inclusive Early College Program accessible to high-need students in particular. This collaborative approach highlights the importance of fostering collaboration among both internal and external partners of Institutions of Higher Education (IHE). By sharing insights into the program design and implementation, the article aims to inspire similar initiatives and contribute to the ongoing dialogue promoting early college experiences for all.
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Research in Mathematics Education.This change reflects the journal's expanding scope, integrating both theoretical and practical aspects of mathematics education in alignment with growing interdisciplinary and applied academic trends.In this editorial, we discuss revised scope of MERP and invite contributions from a diverse range of researchers and practitioners
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Women remain significantly underrepresented in the construction industry, particularly in the skilled trades. Through qualitative exploratory interviews with six women, this study investigates the career trajectories, worksite barriers, and motivational influences shaping women’s experiences in the construction skilled trades. The research is framed using Donald Super’s Life-Span, Life-Space theory and expectancy-value theory (EVT) to explore how career stages and career value affect women’s experiences. Participants described gender bias, limited mentorship, and restricted advancement opportunities as primary challenges. This study highlights the need for industry-led initiatives to increase early exposure to trades, improve mentorship and sponsorship programs, and create structured pathways for career advancement.
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This commentary addresses a problem of practice related to student disengagement in technology-rich classrooms, where learners are digitally connected but socially and academically disconnected. Although not an empirical study, the commentary draws on instructional examples from secondary- and graduate-level teaching. The authors examine how digital literacy instruction can strengthen engagement, reading comprehension, and ethical participation in online environments. The article highlights strategies such as the workshop model, multimodal composition, digital content curation, and the use of mentor texts to support critical thinking and collaborative learning. These practices aim to develop students’ analytical skills, awareness of audience, and recognition of their own positionality in digital spaces. Across courses, the authors reflected on increased student engagement when digital tools were used not simply for task completion but to support inquiry, discourse, and authentic creation for real audiences.
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Objective: Research on use of geosocial networking (GSN) applications (e.g. Grindr, Tinder) by sexual minorities has primarily focused on risky behavior and negative health outcomes (e.g. sexually transmitted infections/HIV, drugs, alcohol, violence) among men who have sex with men. Taking a sex-positive approach, this study aimed to understand how sexual minority GSN app users in the UK and USA perceive impacts on their health and how they manage potential risks. Differences between countries and genders are explored. Design and methods: Qualitative, cross-cultural study in Merseyside (UK) and Connecticut (USA). Photo-elicitation (fake dating profiles) was used in semi-structured interviews conducted with app users seeking same gender partners (n = 31; 15 women, and 16 men) in 2018-2019. Participants were recruited through local LGBTQ+ organizations, social media and from a previous survey, within a quota sampling framework. Transcripts were analyzed using reflexive thematic analysis. Results: Perceived positive health impacts included social and romantic/sexual connections, boosts to self-esteem, and pleasurable sexual experiences. Some negative outcomes were reported, mainly by men, including rejection and low self-esteem, and racism and discrimination. Participants of all genders used strategies to reduce risks to health. Women were particularly cautious of men on apps. No differences between UK and the USA were noted. Conclusions: GSN apps can enable positive sexual experiences and have the potential to increase social cohesion and improve mental wellbeing for stigmatized sexual minorities. All participants took measures to protect both their physical safety and mental wellbeing. Using a sex-positive health promotion approach could empower app users to build on their personal strengths and resources. Although GSN app companies may need to do more to tackle discrimination, apps show a promising opportunity for reducing isolation and health inequities. The similarity of the findings in both areas suggests evidence from the USA may be applicable in the UK.
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The prevalence of Raynaud phenomenon (RP), defined as skin color changes on acral body segments in response to cold or stress, has been estimated to be 3-5% in population studies.1,2 In 80-90% of cases, patients are otherwise healthy and are diagnosed with primary RP.1,3
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