bluuebunny/crossref_metadata_2025_split huggingface dataset:
Altars, palm-trees, and Sourvinou-Inwood’s methodology
Authors: Konstantinou Ariadne 
Published: January 2025

ABSTRACT
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

Abstract

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

Abstract

Summary
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

Abstract
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

ABSTRACT

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 &lt;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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract

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

Abstract

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 &lt; .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

Abstract

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.