bluuebunny/crossref_metadata_2025 huggingface dataset:
Assembly strategy for inclined-holes based on vision and force
Authors: Yang Lu , Xie Chong , Yang Hongchao , Zhan Hong , Qin Lang
Published: January 2025

In robotic part assembly, the unpredictability of part orientations, uncontrollable contact forces, and challenges in maintaining horizontal assembly holes constrain the practical application of robotic assemblies. These factors frequently lead to misalignment, resulting in assembly failures or excessive contact forces that can damage workpieces or robots, thereby increasing economic costs. Consequently, this paper investigates compliant assembly using machine vision, focusing on cylindrical hole assembly. It examines posture estimation for inclined holes. A hole positioning strategy is formulated, comprising a visual initial location stage and a force feedback searching stage, which achieves low-cost and precise positioning of hole parts. To overcome the jamming issues associated with traditional impedance control strategies during the hole insertion stage, a variable compliance center impedance control strategy is introduced. Four experimental setups involving different-sized pegs and holes for inclined holes were developed, the assembly success rate is 94% and 92% when the inclinations of the hole is 30° and 45°, and the peg-in-hole gap is 0.2 mm. The findings confirm that this strategy can accurately complete robotic peg-in-hole automated assembly, address the challenge of inclined hole angles, and improve the precision and efficiency of fully automated robotic assembly with reduced environmental constraints, supporting cost-effective, precise assembly in industrial applications.
Assessment of strength enhancement and structural performance in fiber-reinforced concrete with varying fiber types and percentages
Authors: Mishra Neeti , Srivastava Rajendra Kumar , Varma Rakesh
Published: January 2025

This study investigates the strength-enhancing capabilities of steel fibers, polypropylene fibers, and asbestos fibers in improving the tensile strength, durability, and load-bearing capacity of concrete structures. Experimental results demonstrate that steel fibers, with a tensile strength of up to 1,100 MPa, effectively reduce crack propagation and increase tensile strength by up to 45% at an optimal volume fraction of 1.5%. Polypropylene fibers, when added at 0.9% by volume, enhance ductility and impact resistance, resulting in a 25% improvement in flexural strength compared to plain concrete. Although asbestos fibers are less commonly used due to health concerns, their inclusion at 0.5% by volume was found to provide a 30% increase in fire resistance and a 20% improvement in tensile strength. The study also reveals that an excessive percentage of fibers can reduce workability and compromise the homogeneity of the concrete mix. The findings highlight the importance of optimizing fiber type and volume fraction to achieve a balance between enhanced mechanical properties and practical workability, ensuring concrete’s suitability for specific structural applications.
Tube-MPC based trajectory tracking control for substation inspection robot
Authors: Zuo Dongsheng , Zhao Yongjia , Zhang Wei , Sun Bing
Published: January 2025

A Tube-MPC based trajectory tracking control method was developed to enhance the capabilities of substation inspection robots. First, the kinematic models of the inspection robots were established, and the general form of the optimization control problem for Tube-MPC was introduced. The nominal control law for the nominal system was derived using a linearized nominal model, which was employed to solve the Tube-MPC cost function, ensuring accurate tracking of the desired trajectory. The algorithm was then simulated and tested. Simulation results demonstrate that the Tube-MPC approach significantly outperforms conventional MPC algorithms in terms of trajectory tracking performance and robustness for substation inspection robots. Experimental results further confirm that the Tube-MPC based method effectively enhances both robustness and tracking accuracy during inspection robot operations.
Enhancing text summarization and audio generation using hybrid model
Authors: Koreddi Venkatesh , Chandini Shaik , Challa B V T Kalyan , Sai Ram Teja M
Published: January 2025

In today’s fast-paced world, efficiently processing the vast amount of information in lengthy documents poses significant challenges. Traditional methods of reading and understanding multi-page documents, often spanning six to seven pages, are time-consuming and cumbersome for students, scholars, and professionals who face constant time constraints. This project introduces a novel approach by integrating advanced text summarization with real-time audio generation. Unlike existing solutions, which either focus on summarization or audio conversion separately, this dual-system solution uniquely combines both, allowing users to quickly grasp key content and consume it in audio form while on the move. The summarization component effectively condenses large documents into concise summaries, preserving the critical information and context. Meanwhile, the audio generation component transforms these summaries into speech, enhancing accessibility for auditory learners and users on the go. This innovative combination not only saves time but also offers flexibility, catering to diverse user preferences and learning styles.
Introduction
Authors: Gurney Peter , Grant Matthew , Morley Joel
Published: January 2025

Mass conscription shaped the early lives of a generation of young men as well as society more broadly in early post-war Britain, though its effects have been generally overlooked by historians. The introduction outlines the novel approach to these possible effects developed in the book, which is particularly concerned with how the experience of conscription has been reworked and understood in the memories of participants. It discusses the sources and methods employed, drawing attention especially to the interviewing process and inter-subjectivity, the importance of generational sensibility, life story methodology in oral history, the notion of composure and our preferred stress on contradiction, and interviewees’ agency in constructing their own narratives.
National Service in Popular Culture
Authors: Gurney Peter , Grant Matthew , Morley Joel
Published: January 2025

Representations of national service featured in various popular cultural forms in the post-war period, including films, novels and plays, which this chapter considers. It focusses particularly on the ways in which participants recalled or else failed to recall such representations and ponders what this might tell us about interviewees’ memory of conscription. An important theme that drew together cultural representations and popular memory was humour, with many interviewees emphasising the comedic aspects of conscription. However, they were also invariably keen to contest such representations as misleading for downplaying the serious – and historically significant – reality of their service lives.
Shadows of War
Authors: Gurney Peter , Grant Matthew , Morley Joel
Published: January 2025

The experience of living through the Second World War deeply affected interviewees’ childhood recollections. First, positive memories of wartime are discussed in this chapter, as for many this phase was remembered as an exciting phase marked by freedom and adventure. The tone of participants’ war talk is considered, as they sought to smooth over difficult or psychologically traumatic memories or emphasise how aerial bombardment and evacuation had made them more resilient, especially compared to later generations. Particular attention is paid to how their accounts were frequently marked by ambivalence, as individuals struggled to tell an uplifting story that conformed to ‘good war’ myth.
Authority and Discipline
Authors: Gurney Peter , Grant Matthew , Morley Joel
Published: January 2025

Interviewees’ young lives were enmeshed within power structures over which they had little control. They vividly recalled the moral training they had received from their mothers especially, as well as the physical punishments they had frequently endured. While most recalled their experiences humorously, some individuals unfortunate enough to have had brutal fathers did not. They were also subject to often strict discipline outside the home in their communities, schools, workplaces and voluntary organisations, the influence of which is explored. In the interviews, the theme of individual self-discipline was often bound up within wider narratives about generational and social change.
Remembering the Myth of Classlessness
Authors: Gurney Peter , Grant Matthew , Morley Joel
Published: January 2025

The dominant myth of national service was that it effaced class differences, and many participants fully subscribed to that myth and were indeed adamant that class differences were rendered insignificant by mass conscription. Preferring to talk instead about ‘background’, income and education, they often skirted around talking about class. Snobbery was recalled with abhorrence, however, troubling as it did the idea of classlessness, though ‘ordinariness’ was not held up as the approved norm either. The idea of ‘respect’, which transcended class, was invoked by many individuals, some of whom recalled with fondness moments when class barriers were suspended temporarily.
Social Mobility and Working Life
Authors: Gurney Peter , Grant Matthew , Morley Joel
Published: January 2025

Our participants lived through and benefited from the ‘golden age’ of social mobility in post-war Britain. They reflected on the relationship between their national service and their subsequent working lives and social trajectories, particularly whether and in what ways it had helped them ‘get on’. The importance of the need for rank and authority, in the workplace as well as in the military, came across strongly. Three individual case studies add more depth to the discussion. The role played by cultural capital in facilitating social mobility is stressed, as is the way national service gave some recruits from working-class backgrounds who had been failed by grammar schools another chance to improve their social position.
Imagining and Performing Masculinities
Authors: Gurney Peter , Grant Matthew , Morley Joel
Published: January 2025

There was a widely held idea in post-war Britain that national service would ‘make a man of you’, which shaped interviewees’ recollections. Men spoke about the man-making rituals they experienced as conscripts in relation to changing ideas and practices of masculinity they encountered across the life course. The chapter emphasises the importance of practice over cultural scripts. It dwells on the role of often quite brutal basic training but also the way that was subsequently modified as the regime softened, allowing for the expression of a variety of masculinities. Moreover, despite the approval of certain modes masculine conduct, the connection with military valour was rejected by the majority of interviewees.
Regulating Sexuality and Family Life
Authors: Gurney Peter , Grant Matthew , Morley Joel
Published: January 2025

Interviewees were encouraged to talk about changing ideas of sexuality during national service and across the life course. They had lived through a period of accelerating change in this as in other respects, the tension between past and present particularly apparent in many interviews. National service opened the eyes of some to homosexuality for the first time; some developed attitudes that were more liberal; a minority became more intolerant. Prostitution was another issue that provoked strong reactions, though the tendency was to approve certain ‘respectable’ forms of sexual behaviour over others. Most men desired ‘clean’ girlfriends and well-ordered family lives, and pursued these ambitions after national service.
Political Identities
Authors: Gurney Peter , Grant Matthew , Morley Joel
Published: January 2025

National servicemen’s opinions ranged across the political spectrum. Uniting them was a significant belief in British ‘decline’ in a general sense, with a strong nostalgic colouring and anger at wider processes of change. For many, the key turning point was the perceived crises of the 1970s and the 1980s, which overturned the political and economic certainties of their youth and young manhood. Their analysis of political change, however, relies on popular myths of the period revealing the continuing power of such formations to shape contemporary political opinion. In the end, our cohort’s political views were coloured by an ideal of a lost world of British power and economic security, replaced by a globalised economy and profound mistrust in politics.
Nation, Race, and Immigration
Authors: Gurney Peter , Grant Matthew , Morley Joel
Published: January 2025

Former national servicemen had complex views in the issues of national identity and the intersections of race, immigration and Britain’s relationship with Europe. Often deeply held, their views were framed by their experience of military service, which was mined for corroborative ‘evidence’. What emerges is a profound sense of an exclusively white cohort of elderly men seeking to make sense of a society which had undergone enormous changes. Uniting the majority, however, was a belief in a sense of Britishness defined by values and standards of behaviour (‘decency’, ‘respect’), which could be construed either in a narrow, exclusionary sense or in much more open and inclusive ways.
Diffuse expression of p16 in pancreatic neuroendocrine tumors (PanNETs) and the association of morphology variants
Authors: Yablonski John , Shi Chanjuan , Chen Wei
Published: January 2025

Objective

Distinguishing grade 3 pancreatic neuroendocrine tumors (PanNETs) from neuroendocrine carcinomas (PanNECs) is sometimes challenging. Recently, a diffuse p16-positive pattern was reported in PanNECs but not in grade 3 PanNETs, suggesting that p16 could help differentiate these entities. This study aimed to investigate p16 expression in PanNETs of various grades and its association with clinicopathologic features.

Methods

A total of 114 PanNETs were selected, and their H&E resection slides were reviewed for pathologic features, with a focus on morphologic variants. Tissue microarrays were constructed, and p16 immunohistochemistry was performed. The results were categorized as diffuse positive, partial positive, or negative. Patient electronic health records were reviewed for follow-up data.

Results

Among the 114 PanNETs reviewed, 13 (11.4%) exhibited diffuse p16 expression, 40 (35.1%) were negative, and 61 (53.5%) had partial expression. Diffuse p16 expression occurred in 6 of 38 (15.8%) grade 1, 6 of 60 (10.0%) grade 2, and 1 of 16 (6.3%) grade 3 tumors. Expression did not differ substantially with patient demographics, tumor size, grading, staging, or survival, but diffuse p16 expression was more frequent in body/tail tumors (12/65 [18.5%], P = .019) and in stromal-rich tumors (10/23 [43.5%], P < .001).

Conclusions

Diffuse p16 expression is not uncommon in PanNETs and may be associated with stroma-rich variants.
Bridging the continuity: Practice-enhancing publications about the ambulatory care medication-use process in 2023
Authors: Gazda Nicholas P , Vest Tyler A , Peek Grayson K , Francart Suzanne J , Eckel Stephen F
Published: January 2025

Disclaimer

In an effort to expedite the publication of articles, AJHP is posting manuscripts online as soon as possible after acceptance. Accepted manuscripts have been peer-reviewed and copyedited, but are posted online before technical formatting and author proofing. These manuscripts are not the final version of record and will be replaced with the final article (formatted per AJHP style and proofed by the authors) at a later time.

Purpose

This article identifies, summarizes, and prioritizes published literature on the ambulatory care medication-use process (ACMUP) from 2023 that can describe ambulatory pharmacy practice. The medication-use process is the foundational system that provides the framework for safe medication utilization within the healthcare environment. The ACMUP is defined in this article as having the following components: transitions of care, prescribing, access, dispensing, adherence, and evaluating. Articles evaluating at least one step of the ACMUP were assessed for their usefulness toward practice improvement.

A PubMed search was conducted in January 2024 for the publication year 2023 using targeted Medical Subject Headings (MeSH) keywords and the table of contents of selected pharmacy journals, providing a total of 2,903 articles. A thorough review identified 52 potentially practice-enhancing articles: 6 for transitions of care, 11 for prescribing, 5 for access, 6 for dispensing, 8 for adherence, and 16 articles for evaluating. Trends gleaned from the highest-impact articles are described.

Conclusion

It is important to routinely review the published literature and to incorporate significant findings into daily practice. This article continues a series of articles defining and evaluating the currently published literature around the ACMUP. As healthcare continues to advance and care shifts to ambulatory settings, the ACMUP will continue to be a crucial process to evaluate.
Sulla’s 10,000 Cornelii
Authors: Thein Alexander
Published: January 2025

The 10,000 Cornelii were ex-slaves of the proscribed, manumitted and enfranchised by Sulla. Appian, our only source, describes them as Sulla’s clients and argues that their function was to exercise political control in the city of Rome. Scholars treat them as a political gang, bodyguard, or voting block. This article proposes that the 10,000 Cornelii were first informally manumitted by their own proscribed masters. It was a strategy to reduce the value of their confiscated estates and to create a body of clients with a vested interest in regime change to confirm their freedman status and grant them citizenship. It was to remove this threat, not simply to enhance his retinue of clients, that Sulla granted them freedom and citizenship in his own name.
The Cave of Laughlessness, sensory deprivation, and cognitive depletion at Eleusis
Authors: Mackin Roberts Ellie
Published: January 2025

This article explores the intersection of sensory perception, emotional experience, and ritual practice within the ancient Eleusinian Mysteries, specifically focusing on the ‘Cave of Laughlessness’. The author offers a unique perspective on sensory exaggeration, highlighting the heightened awareness of sensory input. The study delves into the experiential aspects of the Mysteries, considering the cognitive and emotional states induced by the rituals. By investigating the sensory manipulation, emotional engagement, and cognitive depletion experienced by initiands (those candidates for initiation), the article sheds light on the complex interplay of sensory experiences and religious significance. The discussion emphasizes the role of the Cave of Laughlessness as a liminal space crucial in the initiatory journey. It examines the sensory and emotional impact it had on ancient worshippers. Through a multidisciplinary approach encompassing archaeology, neurology, and history, this article contributes to a deeper understanding of the sensory dimensions of religious practices in antiquity, offering insights into the ancient mystical experience and its enduring emotional resonance.
Altars, palm-trees, and Sourvinou-Inwood’s methodology
Authors: Konstantinou Ariadne
Published: January 2025

This article belongs to the celebratory issue of BICS on its seventieth anniversary. It reviews the article of Christiane Sourvinou-Inwood published in BICS 32 (1985). I discuss the main points raised in her article about the representation of palm-trees with altars and parthenoi on Attic vases, as well as trace trends and developments of this topic in subsequent research.
Vistla: identifying influence paths with information theory
Authors: Kursa Miron B
Published: January 2025

Motivation

It is a challenging task to decipher the mechanisms of a complex system from observational data, especially in biology, where systems are sophisticated, measurements coarse, and multi-modality common. The typical approaches of inferring a network of relationships between a system’s components struggle with the quality and feasibility of estimation, as well as with the interpretability of the results they yield. Said issues can be avoided, however, when dealing with a simpler problem of tracking only the influence paths, defined as circuits relying on the information of an experimental perturbation as it spreads through the system. Such an approach can be formalized with information theory and leads to a relatively streamlined, interpretable output, in contrast to the incomprehensibly dense ‘haystack’ networks produced by typical tools.

Results

Following this idea, the paper introduces Vistla, a novel method built around tri-variate mutual information and data processing inequality, combined with a higher-order generalization of the widest path problem. Vistla can be used standalone, in a machine learning pipeline to aid interpretability, or as a tool for mediation analysis; the paper demonstrates its efficiency both in synthetic and real-world problems.

Availability and implementation

The R package implementing the method is available at https://gitlab.com/mbq/vistla, as well as on CRAN.
mettannotator: a comprehensive and scalable Nextflow annotation pipeline for prokaryotic assemblies
Authors: Gurbich Tatiana A , Beracochea Martin , De Silva Nishadi H , Finn Robert D
Published: January 2025

In recent years, there has been a surge in prokaryotic genome assemblies, coming from both isolated organisms and environmental samples. These assemblies often include novel species that are poorly represented in reference databases creating a need for a tool that can annotate both well-described and novel taxa, and can run at scale. Here, we present mettannotator—a comprehensive, scalable Nextflow pipeline for prokaryotic genome annotation that identifies coding and noncoding regions, predicts protein functions, including antimicrobial resistance, and delineates gene clusters. The pipeline summarizes these results in a GFF (General Feature Format) file that can be easily utilized in downstream analysis or visualized using common genome browsers. Here, we show how it works on 200 genomes from 29 prokaryotic phyla, including isolate genomes and known and novel metagenome-assembled genomes, and present metrics on its performance in comparison to other tools.

Availability and implementation

The pipeline is written in Nextflow and Python and published under an open source Apache 2.0 licence. Instructions and source code can be accessed at https://github.com/EBI-Metagenomics/mettannotator. The pipeline is also available on WorkflowHub: https://workflowhub.eu/workflows/1069.
Multifunctional metal–organic frameworks as promising nanomaterials for antimicrobial strategies
Authors: Li Qian-Jin , Xing Fei , Wu Wen-Ting , Zhe Man , Zhang Wen-Qian , Qin Lu , Huang Li-Ping , Zhao Long-Mei , Wang Rui , Fan Ming-Hui , Zou Chen-Yu , Duan Wei-Qiang , Li-Ling Jesse , Xie Hui-Qi
Published: January 2025

Bacterial infections pose a serious threat to human health. While antibiotics have been effective in treating bacterial infectious diseases, antibiotic resistance significantly reduces their effectiveness. Therefore, it is crucial to develop new and effective antimicrobial strategies. Metal–organic frameworks (MOFs) have become ideal nanomaterials for various antimicrobial applications due to their crystalline porous structure, tunable size, good mechanical stability, large surface area, and chemical stability. Importantly, the performance of MOFs can be adjusted by changing the synthesis steps and conditions. Pure MOFs can release metal ions to modulate cellular behaviors and kill various microorganisms. Additionally, MOFs can act as carriers for delivering antimicrobial agents in a desired manner. Importantly, the performance of MOFs can be adjusted by changing the synthesis steps and conditions. Furthermore, certain types of MOFs can be combined with traditional photothermal or other physical stimuli to achieve broad-spectrum antimicrobial activity. Recently an increasing number of researchers have conducted many studies on applying various MOFs for diseases caused by bacterial infections. Based on this, we perform this study to report the current status of MOFs-based antimicrobial strategy. In addition, we also discussed some challenges that MOFs currently face in biomedical applications, such as biocompatibility and controlled release capabilities. Although these challenges currently limit their widespread use, we believe that with further research and development, new MOFs with higher biocompatibility and targeting capabilities can provide diversified treatment strategies for various diseases caused by bacterial infections.
Epidemiological risk factors for acute kidney injury outcomes in hospitalized adult patients: a multicenter cohort study
Authors: Takeuchi Tomonori , Rahman A K M F , Ghazi Lama , Moe Orson W , Toto Robert D , Siew Edward D , Neyra Javier A , Gutierrez Orlando M
Published: January 2025

Background

Multiple studies have identified risk factors for acute kidney injury (AKI) in hospitalized patients, but less is known about factors associated with AKI severity, including non-recovery of AKI.

Methods

Retrospective cohort study of adults (≥18 years) hospitalized between 2014 and 2017 at three US academic medical centers. Study outcomes included incidence of AKI and non-recovery from AKI at hospital discharge in those who survived hospitalization. AKI was defined by KDIGO serum creatinine criteria. Non-AKI recovery was defined as persistent AKI stage ≥1 at time of discharge. Multivariable models assessed the association of risk factors for each outcome, focusing on race, diabetes, and obesity (BMI ≥ 30 versus <30 kg/m2), and adjusting for potential confounders.

Results

Among 56 056 patients included in the study (mean age 57, 25% Black, 48% women), 12 954 (23%) developed AKI. In adjusted models, Black race [odds ratio (OR) 1.26, 95% confidence interval (CI): 1.20, 1.32], diabetes (OR 1.14, 95% CI: 1.08, 1.19) and obesity (OR 1.14, 95% CI: 1.10, 1.20) were all associated with incident AKI. A total of 3591 of the 11 672 (30.8%) patients with AKI who survived until discharge had AKI non-recovery. In adjusted models, obesity (OR 1.27, 95% CI: 1.17, 1.39) was independently associated with higher risk of AKI non-recovery at hospital discharge.

Conclusions

Black race, diabetes, and obesity were associated with the development of AKI in hospitalized patients, but only obesity was associated with non-recovery from AKI at hospital discharge. These findings emphasize the growing relevance of obesity as an epidemiological risk factor of AKI.
Avoidance, fear, helplessness: young Africans contemplate a future shaped by climate change
Authors: Iqani Mehita
Published: January 2025

This article considers, and theorises, the negative emotions expressed in discussions about climate change in a project that sought to understand how young adults in Mozambique, South Africa and Kenya articulated their thoughts and feelings on the topic. A literature review synthesises key work on climate communication, emotions and youth in Africa. A detailed discussion of methods (qualitative interviews) is offered. Empirical findings show that three key negatives feelings were expressed: avoidance, fear, and helplessness. Participants claimed to not think about climate change due to other pressing concerns in their lives. Nevertheless, they admitted that they are aware of climate change and deeply fear its impact. Although they know suffering lies ahead, they feel helpless to stop climate change. These sobering findings should be considered in climate change communication research in Africa. The article concludes by theorising the communicative weight of negative emotions as African climate pessimism.
A haplotype-resolved chromosome-level genome assembly of Urochloa decumbens cv. Basilisk resolves its allopolyploid ancestry and composition
Authors: Ryan Camilla , Fraser Fiona , Irish Naomi , Barker Tom , Knitlhoffer Vanda , Durrant Alex , Reynolds Gillian , Kaithakottil Gemy , Swarbreck David , De Vega Jose J
Published: January 2025

Haplotyped-resolved phased assemblies aim to capture the full allelic diversity in heterozygous and polyploid species to enable accurate genetic analyses. However, building non-collapsed references still presents a challenge. Here, we used long-range interaction Hi-C reads (high-throughput chromatin conformation capture) and HiFi PacBio reads to assemble the genome of the apomictic cultivar Basilisks from Urochloa decumbens (2n = 4x = 36), an outcrossed tetraploid Paniceae grass widely cropped to feed livestock in the tropics. We identified and removed Hi-C reads between homologous unitigs to facilitate their scaffolding and employed methods for the manual curation of rearrangements and misassemblies. Our final phased assembly included the 4 haplotypes in 36 chromosomes. We found that 18 chromosomes originated from diploid Urochloa brizantha and the other 18 from either Urochloa ruziziensis or diploid U. decumbens. We also identified a chromosomal translocation between chromosomes 5 and 32, as well as evidence of pairing exclusively within subgenomes, except for a homoeologous exchange in chromosome 21. Our results demonstrate that haplotype-aware assemblies accurately capture the allelic diversity in heterozygous species, making them the preferred option over collapsed-haplotype assemblies.
De-novo Genome Assembly of the Edwardsiid Anthozoan Edwardsia elegans
Authors: Rutlekowski Auston I , Modepalli Vengamanaidu , Ketchum Remi , Moran Yehu , Reitzel Adam M
Published: January 2025

Cnidarians (sea anemones, corals, hydroids, and jellyfish) are a key outgroup for comparisons with bilaterial animals to trace the evolution of genomic complexity and diversity within the animal kingdom, as they separated from most other animals 100s of millions of years ago. Cnidarians have extensive diversity, yet the paucity of genomic resources limits our ability to compare genomic variation between cnidarian clades and species. Here we report the genome for Edwardsia elegans, a sea anemone in the most specious genus of the family Edwardsiidae, a phylogenetically important family of sea anemones that contains the model anemone Nematostella vectensis. The E. elegans genome is 396 Mb in length and predicted to encode approximately 49,000 proteins. We annotated large conservation of macrosynteny between E. elegans and other Edwardsiidae anemones as well as conservation of both microRNAs and ultra conserved noncoding elements previously reported in other cnidarians species. We also highlight microsyntenic variation of clustered developmental genes and ancient gene clusters that vary between species of sea anemones, despite previous research showing conservation between cnidarians and bilaterians. Overall, our analysis of the E. elegans genome highlights the importance of using multiple species to represent a taxonomic group for genomic comparisons, where genomic variation can be missed for large and diverse clades.
A Sox2 enhancer cluster regulates region-specific neural fates from mouse embryonic stem cells
Authors: Tobias Ian C , Moorthy Sakthi D , Shchuka Virlana M , Langroudi Lida , Cherednychenko Mariia , Gillespie Zoe E , Duncan Andrew G , Tian Ruxiao , Gajewska Natalia A , Di Roberto Raphaël B , Mitchell Jennifer A
Published: January 2025

Sex-determining region Y box 2 (Sox2) is a critical transcription factor for embryogenesis and neural stem and progenitor cell (NSPC) maintenance. While distal enhancers control Sox2 in embryonic stem cells (ESCs), enhancers closer to the gene are implicated in Sox2 transcriptional regulation in neural development. We hypothesize that a downstream enhancer cluster, termed Sox2 regulatory regions 2–18 (SRR2–18), regulates Sox2 transcription in neural stem cells and we investigate this in NSPCs derived from mouse ESCs. Using functional genomics and CRISPR–Cas9-mediated deletion analyses, we investigate the role of SRR2–18 in Sox2 regulation during neural differentiation. Transcriptome analyses demonstrate that the loss of even 1 copy of SRR2–18 disrupts the region-specific identity of NSPCs, reducing the expression of genes associated with more anterior regions of the embryonic nervous system. Homozygous deletion of this Sox2 neural enhancer cluster causes reduced SOX2 protein, less frequent interaction with transcriptional machinery, and leads to perturbed chromatin accessibility genome-wide further affecting the expression of neurodevelopmental and anterior–posterior regionalization genes. Furthermore, homozygous NSPC deletants exhibit self-renewal defects and impaired differentiation into cell types found in the brain. Altogether, our data define a cis-regulatory enhancer cluster controlling Sox2 transcription in NSPCs and highlight the sensitivity of neural differentiation processes to decreased Sox2 transcription, which causes differentiation into posterior neural fates, specifically the caudal neural tube. This study highlights the importance of precise Sox2 regulation by SRR2–18 in neural differentiation.
Genetic differentiation in the MAT-proximal region is not sufficient for suppressing recombination in Podospora anserina
Authors: Grognet Pierre , Debuchy Robert , Giraud Tatiana
Published: January 2025

Recombination is advantageous over the long term, as it allows efficient selection and purging deleterious mutations. Nevertheless, recombination suppression has repeatedly evolved in sex- and mating-type chromosomes. The evolutionary causes for recombination suppression and the proximal mechanisms preventing crossing overs are poorly understood. Several hypotheses have recently been suggested based on theoretical models, and in particular that divergence could accumulate neutrally around a sex-determining region and reduce recombination rates, a self-reinforcing process that could foster progressive extension of recombination suppression. We used the ascomycete fungus Podospora anserina for investigating these questions: a 0.8-Mbp region around its mating-type locus is nonrecombining, despite being collinear between the 2 mating types. This fungus is mostly selfing, resulting in highly homozygous individuals, except in the nonrecombining region around the mating-type locus that displays differentiation between mating types. Here, we test the hypothesis that sequence divergence alone is responsible for recombination cessation. We replaced the mat− idiomorph by the sequence of the mat+ idiomorph, to obtain a strain that is sexually compatible with the mat− reference strain and isogenic to this strain in the MAT-proximal region. Crosses showed that recombination was still suppressed in the MAT-proximal region in the mutant strains, indicating that other proximal mechanisms than inversions or mere sequence divergence are responsible for recombination suppression in this fungus. This finding suggests that selective mechanisms likely acted for suppressing recombination, or the spread of epigenetic marks, as the neutral model based on mere nucleotide divergence does not seem to hold in P. anserina.
Psychometric properties of the Chinese version of Everyday Cognition Scale (ECog) in Taiwanese older adults
Authors: Huang Chien-Yu , Hsieh Yu-Wei , Jhang Kai-Ming , Wang Wen-Fu , Chang Chiung-Chih , Chuang I-Ching , Wang Pei-Ning , Hsu Wen-Chun , Cheng Chia-Hsiung
Published: January 2025

Background and Objectives

The Everyday Cognition Scale (ECog) is widely employed for the subjective rating of functional activities of daily living in older adults. This study aimed to examine the psychometric properties of both informant-rated and self-rated ECog in Taiwanese older individuals to assess its applicability in this context.

Research Design and Methods

A total of 1166 subjects, including older adults (n = 583) and their primary caregivers or family members (n = 583), were recruited. Both self-rated and informant-rated ECog assessments were administered twice within a one-month period. The study evaluated internal consistency, test-retest reliability, random measurement error, discriminative validity, construct validity, and concurrent validity using the Mini-Mental State Examination (MMSE) as a gold standard.

Results

The informant-rated ECog demonstrated high internal consistency, acceptable to good test-retest reliability, small to moderate random measurement error, good discriminative validity, and moderate correlations with the MMSE. Additionally, a seven-factor model of the informant-rated ECog was supported. Conversely, the self-rated ECog exhibited high internal consistency, acceptable test-retest reliability, moderate to large random measurement error, adequate discriminative validity, and small correlations with the MMSE. Notably, only the domains of memory, verbal, planning and organization were supported by a one-factor model.

Discussion and Implications

The psychometric properties of the informant-rated ECog surpassed those of the self-rated ECog. However, the self-rated ECog is recommended as a supplementary tool for assessing individuals' awareness of their cognitive function, particularly in the domain of memory.
Circulating and Magnetic Resonance Imaging Biomarkers of Intestinal Fibrosis in Small Bowel Crohn’s Disease
Authors: Dillman Jonathan R , Tkach Jean A , Fletcher Joel G , Bruining David H , Lu Aiming , Kugathasan Subra , Alazraki Adina L , Knight-Scott Jack , Stidham Ryan W , Adler Jeremy , Minar Phillip , Trapnell Bruce C , Bonkowski Erin L , Jurrell Holden , Lopez-Nunez Oscar , Collins Margaret H , Swanson Scott D , Fei Lin , Qian Lucia , Towbin Alexander J , Kocaoglu Murat , Anton Christopher G , Imbus Rebecca A , Dudley Jonathan A , Denson Lee A
Published: January 2025

Background

We previously identified circulating and MRI biomarkers associated with the surgical management of Crohn’s disease (CD). Here we tested associations between these biomarkers and ileal resection inflammation and collagen content.

Methods

Fifty CD patients undergoing ileal resection were prospectively enrolled at 4 centers. Circulating CD64, extracellular matrix protein 1 (ECM1), GM-CSF autoantibodies (GM-CSF Ab), and fecal calprotectin were measured by ELISA. Ileal 3-dimensional magnetization transfer ratio (3D MTR), modified Look-Locker inversion recovery (MOLLI) T1 relaxation, diffusion-weighted intravoxel incoherent motion (IVIM), and the simplified magnetic resonance index of activity (sMaRIA) were measured by MRI. Ileal resection specimen acute inflammation was graded, and collagen content was measured quantitatively using second harmonic imaging microscopy. Associations between biomarkers and ileal collagen content were tested.

Results

Median (interquartile range [IQR]) age was 19.5 (16-33) years. We observed an inverse relationship between ileal acute inflammation and collagen content (r = −0.39 [95% confidence interval {CI}: −0.61, −0.10], P = .008). Most patients (33 [66%]) received biologics, with no variation in collagen content with treatment exposures. In the univariate analysis, CD64, GM-CSF Ab, fecal calprotectin, and sMaRIA were positively associated with acute inflammation and negatively associated with collagen content (P < .1). The multivariable model for ileal collagen content (R2 = 0.31 [95% CI: 0.11, 0.52]) included log CD64 (β = −.27; P = .19), log ECM1 (β = .47; P = .06), log GM-CSF Ab (β = −.15; P = .01), IVIM f (β = .29, P = .10), and IVIM D* (β = 1.69, P = .13).

Conclusions

Clinically available and exploratory circulating and MRI biomarkers are associated with the degree of inflammation versus fibrosis in CD ileal resections. With further validation, these biomarkers may be used to guide medical and surgical decision-making for refractory CD.
Long-term effect of pharmacological treatment on academic achievement of Norwegian children diagnosed with ADHD: a target trial emulation
Authors: Varnet Pérez Tomás , Øvergaard Kristin Romvig , Frigessi Arnoldo , Biele Guido
Published: January 2025

Background

Attention-deficit/hyperactivity disorder (ADHD) is one of the most commonly diagnosed mental disorders in children. For many patients, treatment involves long-term medication in order to reduce symptoms, regulate behaviour, and, hopefully, improve school performance and achievement. However, there is little to no evidence to support a long-term effect on the latter complex outcomes.

Methods

We utilize a target trial framework to emulate a pretest–posttest control group design and estimate the intention-to-treat effect of ADHD medication on national test scores in children diagnosed with ADHD born between 2000 and 2007 in Norway. The data were obtained through linkage of Norwegian registries (NorPD, Norwegian Prescription Database; NPR, Norwegian Patient Registry; KUHR, Database for Control and Payment of Health Reimbursement; SSB, Statistics Norway; MBRN, Medical Birth Registry of Norway).

Results

The resulting analytic sample size consisted of 8548 children diagnosed with ADHD, with about 9% missingness in their grade eight national test scores. We find that initiating ADHD medication had a slight positive average effect on national test scores for all three domains: English, numeracy, and reading [standardized mean differences: 0.037 (95% compatibility interval (CI95), −0.003; 0.076), 0.063 (CI95, 0.016; 0.111), 0.071 (CI95, 0.030; 0.111), respectively].

Conclusion

We conclude that the estimated long-term average effect of ADHD medication on learning, as measured by the Norwegian national tests, is not clinically relevant. Study strengths include the use of real-world data on ecologically valid and relevant outcomes and the robustness of results across model specifications. Limitations include possibility of unobserved confounding and lack of prescription data.
Single-cell sequencing of human Langerhans cells identifies altered gene expression profiles in patients with atopic dermatitis
Authors: Tamminga Sara M , Van Der Wal M Marlot , Saager Elise S , Van Der Gang Lian F , Boesjes Celeste M , Hendriks Astrid , Pannekoek Yvonne , De Bruin Marjolein S , Van Wijk Femke , Van Sorge Nina M
Published: January 2025

Atopic dermatitis (AD) is characterized by dysregulated T cell immunity and skin microbiome dysbiosis with predominance of Staphylococcus aureus, which is associated with exacerbating AD skin inflammation. Specific glycosylation patterns of S. aureus cell wall structures amplify skin inflammation through interaction with Langerhans cells (LCs). Nevertheless, the role of LCs in AD remains poorly characterized. Here, we performed single cell RNA sequencing of primary epidermal LCs and dermal T cells, isolated from skin biopsies of AD patients and healthy control subjects, alongside specific glycoanalysis of S. aureus strains isolated from the AD lesions. Our findings revealed 4 LC subpopulations ie, 2 steady-state clusters [LC1 and LC1H] and 2 proinflammatory/matured subsets [LC2 and migratory LCs]. The latter 2 subsets were enriched in AD skin. AD LCs showed enhanced expression of C-type lectin receptors, the high-affinity IgE receptor, and activation of prostaglandin and leukotriene biosynthesis pathways, upregulated transcriptional signatures related to T cell activation pathways, and increased expression of CCL17 compared with healthy LCs. Correspondingly, T helper 2 and T regulatory cell populations were increased in AD lesions. Complementary, we performed bulk RNA sequencing of primary LCs stimulated with the S. aureus strains isolated from the AD lesions, which showed upregulation of T helper 2–related pathways. Our study provides proof-of-concept for a role of LCs in connecting the S. aureus–T cell axis in the AD inflammatory cycle.
Vinogradov’s Theorem for Primes With Restricted Digits
Authors: Leng James , Sawhney Mehtaab
Published: January 2025

Let $g$ be sufficiently large, $b\in \{0,\ldots ,g-1\}$, and $\mathcal{S}_{b}$ be the set of integers with no digit equal to $b$ in their base $g$ expansion. We prove that every sufficiently large odd integer $N$ can be written as $p_{1} + p_{2} + p_{3}$ where $p_{i}$ are prime and $p_{i}\in \mathcal{S}_{b}$.
On the Clustering of Padé Zeros and Poles of Random Power Series
Authors: Dostoglou Stamatis , Valettas Petros
Published: January 2025

We estimate non-asymptotically the probability of uniform clustering around the unit circle of the zeros of the $[m,n]$-Padé approximant of a random power series $f(z) = \sum _{j=0}^\infty a_{j} z^{j}$ for $a_{j}$ independent, with finite first moment, and Lévy function $ {\mathcal L}(a_{j}, \varepsilon ) =\sup _{t\in \mathbb R} \mathbb{P}(|a_{j} -t|<\varepsilon )$ satisfying ${\mathcal L}(a_{j}, \varepsilon ) \leq K\varepsilon $. Under the same assumptions we show that almost surely $f$ has infinitely many zeros in the unit disc, with the unit circle serving as a natural boundary for $f$. For $R_{m}$ the radius of the largest disc containing at most $m$ zeros of $f$, the poles of the $[m,n]$-Padé approximant almost surely cluster uniformly at the circle of radius $R_{m}$ as $n \to \infty $ and $m$ stays fixed, and we provide almost sure rates of converge of these $R_{m}$’s to $1$. We also show that our results on the clustering of the zeros hold for log-concave vectors $(a_{j})$ with not necessarily independent coordinates.
Supporting equitable access to kidney transplant in remote Western Australia using continuous quality improvement
Authors: Stewart Felicity , Corsair Nicholas , Stacey James , Cox Sarah , Bowring Joshua , Patankar Khalil , Lee Iann , Teasdale Kristan , Griffiths Emma
Published: January 2025

Background: Despite an epidemic of end-stage kidney disease in the Australian Aboriginal and Torres Strait Islander population, disparities in access to kidney transplantation persist. The journey to a successful kidney transplant is long, with an initial suitability assessment required before waitlist-specific activities begin. In an Aboriginal Community Controlled renal service, we aimed to:

(i) design and implement a continuous quality improvement (CQI) approach to transplant suitability assessment,

(ii) provide transplant suitability assessments for all patients of the service,

(iii) describe what temporary contraindications to kidney transplantation should be the focus of health service improvements,

(iv) explore participant experiences with the suitability assessment process, and

(v) use our findings to inform pre- and post-transplant model of care development within Kimberley Renal Services.

Methods: Mixed methods design with file review. Transplant suitability assessment results with descriptive analysis and semi-structured interview with thematic analysis.

Results: Of completed assessments, 20/66 (30%) had no contraindications and were cleared for workup with median time on dialysis prior to assessment of 2.9 years, 42/66 (64%) had temporary contraindications, and 4/66 (6%) had permanent contraindications. Eighty-five temporary contraindications were identified in 46 individuals: 17/46 had both medical and nonmedical contraindications, 5/46 had medical contraindications only, and 24/46 had nonmedical contraindications only. The most common temporary contraindications were smoking (23/46), treatment adherence (17/46), and high body mass index (11/46). Patients wanted more information on the transplant process, and interviewers noted the importance of providing information in an appropriate way. Patients wanted more support to address modifiable health risk factors to improve their chances of future transplantation.

Conclusions: In the first stages of our CQI approach to improving access to kidney transplants for Kimberley Aboriginal people, we achieved substantial catch-up in suitability assessments and a comprehensive summary of factors impacting successful waitlisting. Our results are consistent with, and build upon other work in this space, highlighting the importance of involving Aboriginal staff and patients in education and support for prospective recipients.