bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multimodel regional frequency analysis of CMIP extreme precipitation
Authors: Le Gall P , Favre A C , Tuel A , Naveau P 
Published: September 2024

Abstract
A recurrent question in climate risk analysis is determining how climate change will affect heavy precipitation patterns. Dividing the globe into homogeneous sub-regions should improve the modeling of heavy precipitation by inferring common regional distributional parameters. In addition, biases due to model errors in global climate models (GCMs) should be considered to understand the climate response to different forcing effects. Within this context, we propose an efficient clustering algorithm that, compared to classical regional frequency analysis (RFA) techniques, is covariate-free and accounts for dependence. It is based on a new non-parametric dissimilarity that combines both the RFA constraint and the pairwise dependence. We derive asymptotic properties of our dissimilarity estimator, and we interpret it for generalized extreme value distributed pairs. As an application, we cluster annual daily precipitation maxima of 16 GCMs from the coupled model intercomparison project. We combine the climatologically consistent subregions identified for all GCMs. This improves the spatial clusters coherence and outperforms methods either based on margins or on dependence. Finally, by comparing the natural forcings partition with the one with all forcings, we assess the impact of anthropogenic forcing on precipitation extreme patterns.
Return to the Planetary Technosphere
Authors: Peoples Columba 
Published: September 2024

Abstract
This chapter returns to the subject of spheres of (in)security: technosphere, biosphere, ecosphere. It does so as part of wider consideration of the sociotechnical imagination of planetary crisis management in relation to ‘other Earths’—worlds in which fixes for planetary emergency are proposed to be found in designed solutions and infrastructures that variously seek to model, mimic, or even alter ‘nature’. Such proposals, so the chapter argues, are often outgrowths of modes of geoengineering and ‘active planetary management’ as discussed in previous chapters of the book. They work by articulating expanded conceptions of what might constitute human, natural, and technological worlds, sometimes seeking to challenge or remove conventional distinctions between those worlds. Planetary-international politics also often returns in such considerations and proposals too, though, as the chapter seeks to argue—with the limits of modern politics often seen to pose an obstacle to the imagination of future planetary security.
Conclusion
Authors: Peoples Columba 
Published: September 2024

Abstract
This concluding chapter revisits key themes of the book, with a particular focus on the themes of crisis and (re)emergence. Drawing on the work done in the previous chapters, it also reflects on an emergent theme of how planetary crisis and emergency are often bound up with (vexed) questions and considerations of how ‘we’ might manage to survive in the future. These questions and considerations, it is suggested, are at least as notable for the ways in which they ‘co-produce’ a sense of who ‘we’ are as much as for the substance of the answers and fixes they are sometimes accompanied by. By way of ending, the chapter puts forward a concept of ‘fixations’ to denote this aspect of the technopolitics of planetary crisis management.
Automated seminal root angle measurement with corrective annotation
Authors: Smith Abraham George , Malinowska Marta , Ruud Anja Karine , Janss Luc , Krusell Lene , Jensen Jens Due , Asp Torben 
Published: September 2024

Abstract
Measuring seminal root angle is an important aspect of root phenotyping, yet automated methods are lacking. We introduce SeminalRootAngle, a novel open-source automated method that measures seminal root angles from images. To ensure our method is flexible and user-friendly we build on an established corrective annotation training method for image segmentation. We tested SeminalRootAngle on a heterogeneous dataset of 662 spring barley rhizobox images, which presented challenges in terms of image clarity and root obstruction. Validation of our new automated pipeline against manual measurements yielded a Pearson correlation coefficient of 0.71. We also measure inter-annotator agreement, obtaining a Pearson correlation coefficient of 0.68, indicating that our new pipeline provides similar root angle measurement accuracy to manual approaches. We use our new SeminalRootAngle tool to identify single nucleotide polymorphisms (SNPs) significantly associated with angle and length, shedding light on the genetic basis of root architecture.
CELEBRIMBOR: core and accessory genes from metagenomes
Authors: Hellewell Joel , Horsfield Samuel T , von Wachsmann Johanna , Gurbich Tatiana A , Finn Robert D , Iqbal Zamin , Roberts Leah W , Lees John A 
Published: September 2024

Abstract

Motivation
Metagenome-Assembled Genomes (MAGs) or Single-cell Amplified Genomes (SAGs) are often incomplete, with sequences missing due to errors in assembly or low coverage. This presents a particular challenge for the identification of true gene frequencies within a microbial population, as core genes missing in only a few assemblies will be mischaracterized by current pangenome approaches.

Results
Here, we present CELEBRIMBOR, a Snakemake pangenome analysis pipeline which uses a measure of genome completeness to automatically adjust the frequency threshold at which core genes are identified, enabling accurate core gene identification in MAGs and SAGs.

Availability and implementation
CELEBRIMBOR is published under open source Apache 2.0 licence at https://github.com/bacpop/CELEBRIMBOR and is available as a Docker container from this repository. Supplementary material is available in the online version of the article.
Generative haplotype prediction outperforms statistical methods for small variant detection in next-generation sequencing data
Authors: O’Fallon Brendan , Bolia Ashini , Durtschi Jacob , Yang Luobin , Fredrickson Eric , Best Hunter 
Published: September 2024

Abstract

Motivation
Detection of germline variants in next-generation sequencing data is an essential component of modern genomics analysis. Variant detection tools typically rely on statistical algorithms such as de Bruijn graphs or Hidden Markov models, and are often coupled with heuristic techniques and thresholds to maximize accuracy. Despite significant progress in recent years, current methods still generate thousands of false-positive detections in a typical human whole genome, creating a significant manual review burden.

Results
We introduce a new approach that replaces the handcrafted statistical techniques of previous methods with a single deep generative model. Using a standard transformer-based encoder and double-decoder architecture, our model learns to construct diploid germline haplotypes in a generative fashion identical to modern large language models. We train our model on 37 whole genome sequences from Genome-in-a-Bottle samples, and demonstrate that our method learns to produce accurate haplotypes with correct phase and genotype for all classes of small variants. We compare our method, called Jenever, to FreeBayes, GATK HaplotypeCaller, Clair3, and DeepVariant, and demonstrate that our method has superior overall accuracy compared to other methods. At F1-maximizing quality thresholds, our model delivers the highest sensitivity, precision, and the fewest genotyping errors for insertion and deletion variants. For single nucleotide variants, our model demonstrates the highest sensitivity but at somewhat lower precision, and achieves the highest overall F1 score among all callers we tested.

Availability and implementation
Jenever is implemented as a python-based command line tool. Source code is available at https://github.com/ARUP-NGS/jenever/
Enhancing the natural absorbing capacity of rivers to restore their resilience
Authors: Wohl Ellen , Fryirs Kirstie , Grabowski Robert C , Morrison Ryan R , Sear David 
Published: September 2024

Abstract
Resilience, which can also be described as absorbing capacity, describes the amount of change that a system can undergo in response to disturbance and maintain a characteristic, self-sustaining regime of functions, processes, or sets of feedback loops. Rivers exhibit varying levels of resilience, but the net effect of industrialized anthropogenic alteration has been to suppress river resilience. As changing climate alters the inputs to rivers and human modification alters the morphology and connectivity of rivers, restoration increasingly considers how to enhance resilience. Characteristics that underpin river absorbing capacity include natural regimes, connectivity, physical and ecological integrity, and heterogeneity. River management emphasizing channel stabilization and homogenization has reduced river absorbing capacity. We propose that the paths to restoring rivers include defining relevant measures of absorbing capacity and understanding the scales of restoration and the sociopolitical elements of river restoration. We provide a conceptual framing for choosing measures that could be used to assess river absorbing capacity.
The relationship between changes in functional connectivity gradients and cognitive–emotional disorders in sudden sensorineural hearing loss
Authors: Li Biao , Xu Xiao-Min , Wu Yuan-Qing , Miao Xiu-Qian , Feng Yuan , Chen Yu-Chen , Salvi Richard , Xu Jin-Jing , Qi Jian-Wei 
Published: September 2024

Abstract
Sudden sensorineural hearing loss, a prevalent emergency in otolaryngology, is known to potentially precipitate cognitive and emotional disorders in affected individuals. Extensive research has documented the phenomenon of cortical functional reorganization in patients with sudden sensorineural hearing loss. However, the potential link between this neural functional remodelling and cognitive–emotional disorders remains unclear. To investigate this issue, 30 bilateral sudden sensorineural hearing loss patients and 30 healthy adults were recruited for this study. We collected clinical data and resting-state functional magnetic resonance imaging data from the participants. Gradient mapping analysis was employed to calculate the first three gradients for each subject. Subsequently, gradient changes in sudden sensorineural hearing loss patients were compared with healthy controls at global, regional and network levels. Finally, we explored the relationship between gradient values and clinical variables. The results revealed that at the global level, sudden sensorineural hearing loss did not exhibit significant differences in the primary gradient but showed a state of compression in the second and third gradients. At the regional level, sudden sensorineural hearing loss patients exhibited a significant reduction in the primary gradient values in the temporal pole and ventral prefrontal cortex, which were closely related to neuro-scale scores. Regarding the network level, sudden sensorineural hearing loss did not show significant differences in the primary gradient but instead displayed significant changes in the control network and default mode network in the second and third gradients. This study revealed disruptions in the functional hierarchy of sudden sensorineural hearing loss, and the alterations in functional connectivity gradients were closely associated with cognitive and emotional disturbances in patients. These findings provide new evidence for understanding the functional remodelling that occurs in sudden sensorineural hearing loss.
Autophagy3D: a comprehensive autophagy structure database
Authors: Neha  , Castin Jesu , Fatihi Saman , Gahlot Deepanshi , Arun Akanksha , Thukral Lipi 
Published: September 2024

Abstract
Autophagy pathway plays a central role in cellular degradation. The proteins involved in the core autophagy process are mostly localised on membranes or interact indirectly with lipid-associated proteins. Therefore, progress in structure determination of ‘core autophagy proteins’ remained relatively limited. Recent paradigm shift in structural biology that includes cutting-edge cryo-EM technology and robust AI-based Alphafold2 predicted models has significantly increased data points in biology. Here, we developed Autophagy3D, a web-based resource that provides an efficient way to access data associated with 40 core human autophagic proteins (80322 structures), their protein-protein interactors and ortholog structures from various species. Autophagy3D also offers detailed visualizations of protein structures, and, hence deriving direct biological insights. The database significantly enhances access to information as full datasets are available for download. The Autophagy3D can be publicly accessed via https://autophagy3d.igib.res.in.
Database URL: https://autophagy3d.igib.res.in
Beta-blockers for secondary prevention following myocardial infarction in patients without reduced ejection fraction or heart failure: an updated meta-analysis
Authors: Chi Kuan-Yu , Lee Pei-Lun , Chowdhury Ishmum , Akman Zafer , Mangalesh Sridhar , Song Junmin , Satish Vikyath , Babapour Golsa , Kang Yi-No , Schwartz Rachel , Chang Yu , Borkowski Pawel , Nanna Michele , Damluji Abdulla A , Nanna Michael G 
Published: September 2024

Abstract

Aims
The 2023 ESC guidelines for acute coronary syndrome note that contemporary data are heterogenous regarding beta-blocker (BB) use post-myocardial infarction (MI) in patients without reduced ejection fraction (EF) or heart failure (HF). We aimed to address the heterogeneity in contemporary data around BB post-MI in this population.

Methods and results
We searched six databases from 1 January 2000 to 1 September 2024 to identify contemporary studies enrolling MI patients without reduced EF (≤40%) or history of HF receiving BB at index MI and comparing outcomes between BB users and non-users. The primary outcome was all-cause mortality. Secondary outcomes included major adverse cardiac and cerebrovascular events (MACCE) and cardiovascular (CV) mortality. Random-effects meta-analysis was conducted using the restricted maximum likelihood method. There were 24 studies including 290 349 patients enrolled in the contemporary era. Overall, BB use was associated with a significant 11% reduction in all-cause mortality [hazard ratio (HR), 0.89; 95% confidence interval (CI), 0.81–0.97; I2 = 40], however with moderate-to-high statistical heterogeneity. Pre-specified subgroup analyses demonstrate comparable all-cause mortality (HR, 0.99; 95% CI, 0.94–1.06; I2 = 0%), CV mortality (HR, 0.99; 95% CI, 0.85–1.15; I2 = 0%), and MACCE (HR, 1.24; 95% CI, 1.01–1.52; I2 = 0%) in patients with a 1-year event-free period, defined as no death, recurrent MI, or HF while on BB following index MI. In patients with no event-free period, meta-regression revealed that BB mortality benefits were modified by the study inclusion period (P = 0.01), reflecting a temporal trend of decreasing BB mortality benefits over time. Based on the temporal trend, in patients with preserved EF post-2010, BB exhibited no reduction in all-cause mortality (HR, 0.97; 95% CI, 0.90–1.04; I2 = 0%), but a non-significant trend towards increased CV mortality (HR, 1.29; 95% CI, 0.96–1.72; I2 = 0%) and a significant increase in MACCE (HR, 1.24; 95% CI, 1.01–1.52; I2 = 0%).

Conclusion
In the contemporary reperfusion era, BB may not confer additional mortality benefits beyond a 1-year event-free period post-MI in patients without reduced EF. Moreover, post-MI BB use was associated with detrimental effects in patients with preserved EF.
Should We Work Smarter or Harder for Our Health? A Comparison of Intensity and Domain-Based Time-Use Compositions and Their Associations With Cognitive and Cardiometabolic Health
Authors: Mellow Maddison L , Dumuid Dorothea , Wade Alexandra , Olds Timothy , Stanford Ty , Keage Hannah , Hunter Montana , Ware Nicholas , Simpson Felicity M , Karayanidis Frini , Smith Ashleigh E 
Published: September 2024

Abstract

Background
Each day is made up of a composition of “time-use behaviors.” These can be classified by their intensity (eg, light or moderate–vigorous physical activity [PA]) or domain (eg, chores, socializing). Intensity-based time-use behaviors are linked with cognitive function and cardiometabolic health in older adults, but it is unknown whether these relationships differ depending on the domain (or type/context) of behavior.

Methods
This study included 397 older adults (65.5 ± 3.0 years, 69% female, 16.0 ± 3.0 years education) from Adelaide and Newcastle, Australia. Time-use behaviors were recorded using the Multimedia Activity Recall for Children and Adults, cognitive function was measured using the Addenbrooke’s Cognitive Examination III and Cambridge Neuropsychological Test Automated Battery, and systolic and diastolic blood pressure, total cholesterol, and waist–hip ratio were also recorded. Two 24-hour time-use compositions were derived from each participant’s Multimedia Activity Recall for Children and Adults, including a 4-part intensity composition (sleep, sedentary behavior, light, and moderate–vigorous PA) and an 8-part domain composition (Sleep, Self-Care, Chores, Screen Time, Quiet Time, Household Administration, Sport/Exercise, and Social).

Results
Linear regressions found significant associations between the domain composition and both Addenbrooke’s Cognitive Examination III (p = .010) and waist–hip ratio (p = .009), and between the intensity composition and waist–hip ratio (p = .025). Isotemporal substitution modeling demonstrated that the domains of sedentary behaviors and PA impacted their associations with Addenbrooke’s Cognitive Examination III, while any PA appeared beneficial for waist–hip ratio.

Conclusions
Findings suggest the domain of behavior should be considered when aiming to support cognitive function, whereas, for cardiometabolic health, it appears sufficient to promote any type of PA.
Effect of structured individual and combined education on blood glucose regulation in type 2 diabetes mellitus
Authors: Arslan Zarif Cagla , Tuzun Sabah , Öner Can , Haciağaoğlu Nazli , Çetin Hüseyin , Şimşek Engin Ersin 
Published: September 2024

Abstract
Although various approaches have been used in diabetes self-management education (DSME) programs, the effect of DSME programs on glycemic control is controversial. This study aimed to compare the effects of structured individual education and combined education on glycemic regulation in type 2 diabetes mellitus (T2DM). This study included T2DM patients who applied to the Ust Kaynarca Diabetes Center between 1 January 2018 and 11 March 2020. All data were retrospectively evaluated from hospital information systems. Patients who received only individual education were defined as the individual education group (IEG), and patients who received both individual and group education were defined as the combined education group (CEG). A total of 496 T2DM patients, with 248 (50.0%) in the IEG and 248 (50.0%) in the CEG, were included in the study. The change in HbA1c (ΔHbA1c) value for the IEG was 1.0% (2.5%), while the ΔHbA1c value for the CEG was 1.9% (2.8%) (P &lt; 0.001). When factors affecting the glycemic control were evaluated, it was determined that the type of education [odds ratio (OR) = 2.295, P &lt; 0.001], gender (OR = 1.799, P = 0.007), presence of hyperlipidemia (OR = 0.559, P = 0.032) and presence of medications added to treatment (OR = 1.558, P = 0.041) were effective on glycemic control. Combined education, in which individual and group education are conducted together, is more effective than individual education in glucose regulation.
Assessment of industry 4.0 readiness in smart manufacturing: evidence for the south African economy
Authors: Inyang Victoria , Kanakana Grace M 
Published: September 2024

Abstract
This study focuses on the significant transformation triggered by Industry 4.0 (14.0) within small and medium-sized enterprises (SMEs) operating in the manufacturing sector. The research aims to explore the readiness and the extent to which I4.0 criteria are integrated into the operations and business models of the South African industry. This study employed a quantitative research approach, with selected industry professionals as participants through purposeful sampling via Google Form distribution. Nineteen semi-structured interviews were subsequently conducted, utilizing an extensive and intricate questionnaire. The collected data was subjected to thematic analysis for comprehensive examination of the responses. The research revealed that I4.0 demands higher skills compared to traditional manufacturing practices. The study offers valuable insights for human resource practitioners and manufacturing professionals. Furthermore, the study establishes a foundation for future research exploring the development of Industry 4.0 skills competencies within the South African industry.
Innovative approaches to scaling up hydrogen production and storage for renewable energy integration
Authors: Kuterbekov Kairat A , Kabyshev Asset , Bekmyrza Kenzhebatyr , Kubenova Marzhan , Kabdrakhimova Gaukhar , Ayalew Abebe T 
Published: September 2024

Abstract
The global imperative to reduce greenhouse gas emissions and phase out fossil fuels has prompted hydrogen to emerge as a critical player in the transition to sustainable energy systems and eco-friendly transport solutions. This study endeavors to examine innovative technologies for hydrogen production and storage, with the objective of overcoming the obstacles that impede their widespread adoption. The integration of hydrogen with renewable energy sources is one of the methods that have been investigated. Specifically, the effectiveness of coupling hydrogen fuel cells with wind or solar power systems has been examined in order to ensure a reliable energy supply and improve grid stability. The results of this study present innovative methods for mass hydrogen production, including electrolysis of water and advanced techniques for extracting hydrogen from fossil fuels while minimizing environmental impact. Additionally, this study evaluates strategies for underground hydrogen storage, considering local geological conditions to optimize storage efficiency and safety. The findings indicate that salt caverns offer a secure and stable hydrogen containment system and have a high storage efficiency of up to 90%. The evaluation of depleted gas fields demonstrated promising results in terms of sealing integrity and storage efficiency (88%). The outcomes provide insights into the feasibility of large-scale hydrogen generation and storage, offering valuable guidance for future energy solutions dependent on hydrogen in diverse geographic contexts.