bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spaces of Nurture and Resistance
Authors: Barylo William 
Published: February 2025

Abstract
Reviving the original spirit of the seventh-century mosque as a community hub, many initiatives set up informal third spaces building communities around the notions of empathy, creativity, and service. Despite their lack of resources and their small scale, displaying unconventional methods of community organizing and governance through consultation and consensus, they are cradles for the development of novel forms of political engagement and showcase sustainable methods for grassroots movements. These marginal spaces in the borderlands of the empire are a practical articulation of the growing movement for Islamic decoloniality, a pluriversal framework free from man-made supremacies, resisting hegemonies, and opening a path to collective healing and flourishing.
Conclusion
Authors: Barylo William 
Published: February 2025

Abstract
The grassroots organizations, community hubs, charities, arts collectives, and individuals in this book demonstrate that, for people at the margins, it is possible to resist new forms of colonizations, and moreover, to heal and flourish, despite the absence of resources, networks, visibility, and political power. They show that even though organic processes take time, it is possible to make a positive difference for their local neighbourhoods and the wider society without engaging with systems of domination and oppression. They have successfully built alternative methods, spaces, and ways of existing that transcend the limitations of class, race, gender, and belief in effect in the neoliberal society.
Introduction: Cultural Geography and the Law of the Sea
Authors: Kraska James , Ryou-Ellison Hayoun 
Published: February 2025

Abstract
This introductory chapter draws on an interdisciplinary understanding of culture and how states interpret their own social history and practices within the same civilizational and cultural zone. We adhere to regional cultural definitions similar to those outlined in Huntington’s classification of political culture in terms of civilizations on the basis of geography and history, as seen in his seminal work, The Clash of Civilizations and the Remaking of World Order. Huntington divided the world into the following civilizations: Western, Orthodox, Latin American, Hindu, greater China (the Confucian Sinosphere), African, Buddhist, and Muslim. In a slight departure from Huntington’s civilization-based categories listed above, we divided the world into regions based on geographical considerations. Our regional categories are Western Europe, Eastern Europe, North America, Latin America, Sub-Saharan Africa, Oceania, East Asia, and South Asia. The regional cultural zones in our analysis are reflected in similar understandings and approaches that inform their own unique approaches to law and policy and which tend to be consistent among states with a shared cultural worldview, as opposed to those of states from traditions outside the civilizational zone in question. For example, Western traditions have focused more on individuality and liberalism, whereas Eastern traditions have placed comparatively greater emphasis on group stability and social harmony. Furthermore, broader patterns are evident beyond their respective cultural spheres and are manifest in the Global North–South developmental dynamic.
South Asia
Authors: Rajput Aniruddha 
Published: February 2025

Abstract
References from ancient writings in South Asia reflect an uninterrupted practice of freedom of navigation and peaceful uses of seas for several centuries and the establishment of trade relations around the world. When Portuguese explorers encountered India, there was already a liberal regime of maritime trade among African, Arabic, and Indian traders in the Indian Ocean. The absolute freedom of navigation and peaceful use of oceans also facilitated movements of religious ideas, pilgrims, and cultures, building cosmopolitan communities from Zanzibar to Myanmar. The Spice Route and European competition led to the eventual loss of political independence of the native kingdoms and the establishment of Portuguese monopoly on the seas. The experience of colonization influenced and radically changed the approach towards the regulation of the sea from complete freedom of navigation to a controlled approach aimed at protecting colonies from predatory colonization by European rivals, such as the Dutch Provinces. These ideas continued to influence the approach of the South Asian States in the development of the law of the sea throughout the colonial era and even brought together the States of the Indian Ocean region during the Third UN Conference on the Law of the Sea. This bloc of States formed the bulwark of the Global South during the negotiations. Over time, the priorities of the States in the Indian Ocean have shifted from a vision of collective governance of the global commons towards States advancing their individual interests based on geopolitical or economic interests.
Positive Garden Aesthetics
Authors: Fenner David 
Published: February 2025

Abstract
The cognitivist environmental-aesthetic theory of Positive Aesthetics—that holds that nature untouched by humans, known through the lens of science, is always aesthetically good—is not relevant to gardens. Nonetheless, I argue that every garden (with one possible exception) is aesthetically positive, that true summative aesthetic judgements about (bona fide) gardens are always on balance positive, and that every garden possesses more aesthetically positive features than negative ones. I offer three arguments for this thesis: (1) once a garden has more negative than positive aesthetic properties, it loses both its design and its purpose; (2) once a garden has more negative than positive aesthetic properties, standard or typical gardening practices are no longer useful for maintaining the garden; and (3) a particular garden that has more negative than positive aesthetic properties is no longer the garden that it was; to bring it back, so to speak, is to redesign and reinstall a new garden.
PharaCon: A new framework for identifying bacteriophages via conditional representation learning
Authors: Bai Zeheng , Zhang Yao-zhong , Pang Yuxuan , Imoto Seiya 
Published: February 2025

Abstract

Motivation
Identifying bacteriophages (phages) within metagenomic sequences is essential for understanding microbial community dynamics. Transformer-based foundation models have been successfully employed to address various biological challenges. However, these models are typically pre-trained with self-supervised tasks that do not consider label variance in the pre-training data. This presents a challenge for phage identification as pre-training on mixed bacterial and phage data may lead to information bias due to the imbalance between bacterial and phage samples.

Results
To overcome this limitation, we proposed a novel conditional BERT framework that incorporates label classes as special tokens during pre-training. Specifically, our conditional BERT model attaches labels directly during tokenization, introducing label constraints into the model’s input. Additionally, we introduced a new fine-tuning scheme that enables the conditional BERT to be effectively utilized for classification tasks. This framework allows the BERT model to acquire label-specific contextual representations from mixed sequence data during pre-training and applies the conditional BERT as a classifier during fine-tuning and we named the fine-tuned model as PharaCon. We evaluated PharaCon against several existing methods on both simulated sequence datasets and real metagenomic contig datasets. The results demonstrate PharaCon’s effectiveness and efficiency in phage identification, highlighting the advantages of incorporating label information during both pre-training and fine-tuning.

Availability
The codes of PharaCon are now available in: https://github.com/Celestial-Bai/PharaCon.

Supplementary information
Supplementary data are available at Bioinformatics online.
RADNet: a highly and robust dynamic network for object detection in complex road scenes
Authors: Zhao Wenyang , Yang Xiaoyao , Wang Yong 
Published: February 2025

Abstract
Aiming at the problems of low detection accuracy and redundant model parameters in the current road scene detection, a RADNet-based road scene detection algorithm is proposed. In this algorithm, an efficient backbone structure CSPResRepBlock is designed to enable the model to obtain more comprehensive target information. Secondly, a multi-feature fusion progressive pyramid is designed to significantly alleviate the elimination of target feature information during the feature fusion process. Meanwhile, a new decoupling head structure called Efficient Dynamic DCNv2 Head is designed, which significantly improves the model’s sensitivity to deformation or edge blurring features. In addition, a structured pruning algorithm is introduced to achieve network acceleration by automatically analyzing complex structural couplings and correctly removing parameters. Finally, experiments on the BDD100K dataset show that the RADNet algorithm improves the average detection accuracy mAP50 by 6.3% and reduces the number of parameters by 68.6% and the computational effort by 30.3% compared to Yolov8s. The inference speed of the model is 114.1 FPS. The model’s generalizability was evaluated using four additional publicly available datasets. These results show that the RADNet algorithm is effective and superior for the task of autopilot target detection.
Clinical outcomes of Kawashima procedure and subsequent hepatic vein incorporation
Authors: Behrend Lea , Matsubara Muneaki , Osawa Takuya , Schaeffer Thibault , Palm Jonas , Niedermaier Carolin , Heinisch Paul Philipp , Piber Nicole , Hager Alfred , Ewert Peter , Hörer Jürgen , Ono Masamichi 
Published: February 2025

Abstract

OBJECTIVES
We aimed to evaluate outcomes after Kawashima procedure with special regard to the development of pulmonary arterio-venous malformations.

METHODS
All patients who underwent Kawashima procedure between 1992 and 2022 were reviewed.

RESULTS
Twenty-one patients underwent Kawashima procedure at a median age of 14.5 (interquartile range, 8.4–40.4) months. There were no hospital deaths and 2 late deaths. Survival after Kawashima procedure at 5, 10, and 15 years was 90.5, 82.9, and 69.1%, respectively. It was 100% at 10 years for children 9 months old or younger at Kawashima procedure, compared with 77.0% for older children (p = 0.281). Hepatic vein incorporation was achieved in 16 patients (76.2%) at a median age of 3.3 (2.7–13.8) years and at a median interval of 2.6 (1.9–8.6) years. Survival after hepatic vein incorporation at 5, 10, and 15 years was 92.3, 83.1, and 55.4%, respectively. Pulmonary arterio-venous malformations developed in 4 patients after Kawashima procedure, which improved after hepatic vein incorporation in 3 patients. Of 4 patients who developed pulmonary arterio-venous malformations after hepatic vein incorporation, 2 patients died, and 2 patients survived. All of them had bilateral superior vena cava and hepatic venous flow was excluded in one lung as the cause of pulmonary arterio-venous malformations.

CONCLUSIONS
Kawashima procedure could be performed with low operative risk on a patient aged less than 9 months. Despite the current early Kawashima and subsequent hepatic vein incorporation strategy, the incidence of pulmonary arterio-venous malformations did not decrease. Therefore, leaving antegrade pulmonary blood flow at Kawashima procedure is recommended.
A method of classifying the influence of intraparticle diffusion in adsorption systems: characteristic curves of the diffusion-chemisorption kinetic model
Authors: Sutherland Clint 
Published: February 2025

Abstract
This review evaluates 70 published studies with R2 &gt; 0.95 that apply the diffusion-chemisorption (D-C) model to adsorption systems. It also incorporates an experimental component to demonstrate the practical applicability of the derived characteristic curves and equations. The study introduces a new framework for classifying adsorption systems based on intraparticle diffusion, leveraging a solid-phase mass transfer index (RDC) and characteristic curves derived from the D-C kinetic model. Additionally, new equations were developed to rapidly estimate the half-time of adsorption reactions and map operating time as a function of sorbent saturation. The characteristic curves based on the published studies revealed four distinct zones for RDC ranging from 0 to infinity. Type I curves correspond to large particle sizes and highly porous adsorbents, whereas Type IV curves represent powdered and low-porosity adsorbents. The concurrence to Types I, II, III, and IV curves from the 70 published studies were 8.5%, 36%, 32.5%, and 23%, respectively. To demonstrate the usefulness of the developed equations, the adsorption of Cu(II) ions by Fomes fasciatus was successfully evaluated to elucidate the influence of intraparticle diffusion and predict adsorption performance. This type of analysis offers a valuable tool for researchers and designers to identify adsorbents for specific adsorbates and explicate transport mechanisms. Further, it minimises the need for extensive sampling and enables the comparison of adsorbent performances.
Association of Life’s Essential 8 and Incident Cardiac Conduction Disorder: a prospective cohort study
Authors: Long Tianxin , Wu Xiaoying , Chen Yongming , Fu Bingqi , Cheng Sijing , Huang Hao , Niu Hongxia , Hua Wei 
Published: February 2025

Abstract

Aims
To evaluate the effect of Life’s Essential 8 (LE8), a comprehensive cardiovascular health (CVH) metric from the American Heart Association, on the risk of cardiac conduction disorders (CCD).

Methods and Results
We conducted a prospective cohort study of 112,160 adults from the UK Biobank, free of cardiovascular disease at baseline, to examine the association between LE8 scores and the risk of CCD. LE8 scores were categorized into low (0-49), moderate (50-79), and high (80-100) CVH groups. Cox proportional hazards models were used to estimate the hazard ratios (HRs) and 95% confidence intervals (CIs) for CCD incidence during a median follow-up of 11.6 years. A total of 2,760 CCD cases were identified. After adjustment for confounders, the high CVH group exhibited a significantly lower risk of CCD compared to the low CVH group (HR: 0.48, 95% CI: 0.40-0.56). Further analyses showed reduced risks for both severe conduction block (HR: 0.63, 95% CI: 0.52-0.78) and left bundle branch or fascicular block (HR: 0.35, 95% CI: 0.25-0.49) in the high CVH group. Restricted cubic spline regression revealed an L-shaped association between LE8 score and CCD risk. Among individual LE8 metrics, WQS analysis revealed that BMI and sleep health were the major contributors to reduced CCD risk.

Conclusions
Higher LE8 scores were associated with a lower risk of CCD, including severe conduction block requiring pacemaker implantation and left bundle branch or fascicular block. Comprehensive strategies targeting optimal CVH, especially BMI and sleep health, may be beneficial for preventing CCD.
Interspecies and Intraspecies “Talk” Shape the Bacterial Biofilms
Authors: Yiyang Lou , Liu Ziqi , Zhang Qiyi , Zhang Lujie , Liao Xinyu , Yang Tian , Liu Donghong , Lu Xiaonan , Ahn Juhee , Ding Tian , Feng Jinsong 
Published: February 2025

Abstract
Bacteria pretend to organize into complex, multicellular structures known as biofilms, which enable survival and adaptation in dynamic environments. Bacterial biofilms serve diverse functions, including providing structural stability, directing metabolic adaptations, and facilitating bacterial expansion and nutrient acquisition. In natural environments, biofilms are predominantly formed by diverse multi-species bacteria. The formation of multi-species biofilms is a dynamic process shaped by intricate bacterial interactions, encompassing both cooperative and antagonistic behaviors. These interactions are mediated by signaling molecules that facilitate cell-to-cell communications, influenced by the spatiotemporal heterogeneity of the extracellular polymeric substance (EPS) matrix and biofilm architecture. This review synthesizes recent advances in understanding bacterial interactions within biofilms, focusing on mediating metabolites, underlying mechanisms, and their implications for the process of biofilm development. These insights offer a foundation for developing strategies to manipulate microbial communities and control biofilm-related challenges.
Loneliness links Adverse Childhood Experiences to Mortality Risk across 26 years
Authors: Curtis Aisling , Kirwan Emma , Luchetti Martina , Creaven Ann-Marie , Turiano Nicholas , McGeehan Máire , Graham Eileen K , O’Súilleabháin Páraic S 
Published: February 2025

Abstract

Objectives
Adverse Childhood Experiences (ACEs) are associated with increased mortality risk. Individuals with a history of certain adversity during childhood tend to report higher levels of loneliness in later life. In our pre-registered study, we examined whether loneliness mediates the ACEs to mortality risk relation.

Methods
Participants were from the Midlife in the United States Survey (N = 4963; M [SD] 46.44 [12.52] years, 53.3% female). Follow-up period spanned 26 years. A comprehensive measure of ACEs was employed consisting of 20 ACEs from five categories: physical abuse, emotional abuse, socioeconomic disadvantage, adverse family structure, and poor health at age 16 years.

Results
ACEs was a significant predictor of mortality risk. Loneliness mediated the ACEs-mortality risk relation. In other words, loneliness in adulthood accounted for the relation between ACEs and future death. These effects withstood a range of sensitivity checks and adjustments for important factors, such as social isolation.

Discussion
Loneliness appears to be a central mechanism in the long-term impact of ACEs on longevity, such that, for adversity during childhood, loneliness experienced during adulthood may be a toxic pathway to future death.
The genome of Vitis vinifera cv. Mgaloblishvili reveals resistance and susceptibility factors to downy mildew in the Rpv29 and Rpv31 loci
Authors: Ricciardi Valentina , Minio Andrea , Massonnet Melanie , Wittenberg Alexander H J , Figueroa-Balderas Rosa , Maghradze David , Toffolatti Silvia Laura , Failla Osvaldo , Cantu Dario , De Lorenzis Gabriella 
Published: February 2025

Abstract
Mgaloblishvili, a grapevine variety from Georgia (Southern Caucasus), exhibits a unique resistance mechanism against downy mildew. Mgaloblishvili resistance mechanism, involving pathogen recognition, activation of ethylene signalling pathway, structural and chemical defences, is mediated by the resistance loci Rpv29, Rpv30, and Rpv31. Mgaloblishvili genome was sequenced using PacBio HiFi, resulting in a chromosome-scale diploid assembly of 986 Mbp, including 58,912 predicted protein-coding genes across two phased chromosome sets. Comparative analysis with the susceptible PN40024 genome allowed us to identify differences in structure, gene content, and gene expression, as well as the impact of structural variants (SVs) and single nucleotide polymorphisms (SNPs) between Mgaloblishvili and PN40024 loci. Resistance haplotypes were identified through DNA sequencing of a self-pollinated Mgaloblishvili population. Compared to orthologous regions in PN40024, the Rpv29 locus in Mgaloblishvili exhibits reduced gene content, while the Rpv31 locus has similar gene content. In both Mgaloblishvili and PN40024, most genes within these loci are associated with plant defence pathways. While genes in both genotypes perform similar functions, SVs and SNPs were identified as key determinants of the structural differences between the genomes. Defining the Rpv30 locus was challenging due to ambiguous marker localization. DNA sequencing allowed us to identify resistance haplotypes for both Rpv30 and Rpv31 on Mgaloblishvili haplotype 2, though insights into the Rpv29 locus remain limited. Our results indicate that Mgaloblishvili's resistance is driven by numerous small SVs and SNPs, which lead to the loss of susceptibility factors and unique transcriptional regulation of defence-related genes.
Natural History of Chapare Virus Infection in Strain 13 Guinea Pigs
Authors: Johnson Dylan M , Fenton Karla A , Dobias Natalie , Geisbert Thomas W , Cross Robert W 
Published: February 2025

Abstract
Chapare virus (CHAPV) is an emerging arenavirus first discovered in Bolivia. Clinical cases have a high case fatality rate and a concerning capacity for person-to-person spread. Animal models of CHHF are needed to study pathogenesis and development of medical counter measures. Here, we present a narrowly focused study describing lethal infection of strain 13 guinea pigs with CHAPV. Animals challenged with CHAPV had progressive weight loss, lymphocytopenia, neutropenia, thrombocytopenia, hepatitis, vascular leakage, and gastrointestinal hemorrhage, resulting in uniform lethality between 7- and 16-days following challenge. This work lays the foundation for development of a small animal model of CHAPV infection.
Patient-reported outcome measures (PROMs) used to assess sexual functioning in prostate cancer patients: a systematic review of psychometric properties
Authors: Abu-Odah Hammoda , Ho Ka-Yan , Ng Chi-Fai , Wu Siyuan , Lam Katherine-Ka-Wai , Yorke Janelle 
Published: February 2025

Abstract

Background
Prostate cancer (PCa) significantly impacts patients’ sexual functioning and quality of life. Patient-reported outcome measures (PROMs) are essential for accurately assessing these issues, yet a comprehensive evaluation of their psychometric properties in PCa patients is lacking.

Aims
This systematic review aimed to provide a comprehensive evaluation of all generic and specific PROMs used to assess sexual functioning in PCa patients and make recommendations the application of PROMs in this patient group.

Methods
Six electronic databases were searched from up to May 5, 2024. Studies reporting the development and/or validation of PROMs for PCa patients or generic instruments administered to this population were included. The COSMIN risk of bias checklist was adopted to assess the methodological quality and psychometric properties of included PROMs. Psychometric properties of the PROM in each included study were rated against the criteria for good measurement properties based on the COSMIN guideline.

Outcomes
The main outcome was to identify the appropriate PROM that can be adopted and used for assessing sexual functioning in PCa patients in clinical setting.

Results
A total of 10 PROMs were identified across 32 studies, primarily focusing on localized PCa patients after radical prostatectomy. The Expanded Prostate Cancer Index Composite (EPIC-26) was the most frequently evaluated and widely used PROM in clinical practice. EPIC-26 (Spanish, Italian, Chinese versions) and UCLA Prostate Cancer Index (UCLA-PCI) demonstrated better psychometric properties compared to other scales. However, no PROM met all COSMIN standards.

Clinical Implications
In a clinical setting, it is crucial to utilize well-validated PROMs with good psychometric properties to effectively identify patients with PCa experiencing sexual difficulties who may require additional support.

Strengths and Limitations
We applied strict inclusion criteria related to study design and study population, ensuring the assumption of transitivity and the consistency of the analysis.

Conclusion
Although EPIC-26 is a shortened version with strong psychometric properties, it may still be too lengthy for patients with significant health issues. Furthermore, the included PROMs do not address issues related to partner relationships, or the psychological impact of sexual dysfunction in sufficient detail. Future research should aim to develop and validate new PROMs that fill these gaps. These tools should be both psychometrically robust and practical for routine use, enabling real-time monitoring and improved care delivery.