bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development of a screening tool for reduced vision among inpatients of hospital rehabilitation units
Authors: Stalin Amritha , Khan Shamrozé , Labreche Tammy , Narayan Abhishek , Christian Lisa W. T. , Stanberry Andre , Leat Susan J. 
Published: February 2025

SIGNIFICANCE
This study developed a practical screening tool to identify reduced habitual vision (RHV) in hospital rehabilitation units. This tool would enhance patient care by enabling timely interventions in resource-limited settings.

PURPOSE
The study aimed to develop a practical and implementable screening tool to identify patients with RHV in hospital rehabilitation units. Potential vision measures, screening questions, and demographic variables were considered to determine the optimum combination.

METHODS
The cross-sectional study recruited 112 adult inpatients (aged 18+ years) from three rehabilitation units in an acute care hospital in Ontario, Canada, between October 2018 and February 2019. Data included an oral questionnaire on demographics, health status, and self-reported vision function, alongside vision assessments (distance visual acuity [VA], contrast sensitivity [CS], visual fields [VFs], and stereopsis). Univariate and multivariate logistic regression analyses were conducted to identify significant predictors of RHV, defined by VA >0.3 logMAR, CS <1.40 logCS, or any VF defect.

RESULTS
The average age of participants was 74.5 years (±14.3 years), and RHV was present in 48.7%. Significant predictors of RHV included self-reported “happiness” with vision with current spectacles and difficulty reading a newspaper. The optimal predictive factors were VA and VF testing (96% sensitivity), but for practical implementation, the combination of three self-reported questions (happiness with vision, difficulty reading a newspaper, and difficulty distinguishing facial expressions) demonstrated 74% sensitivity.

CONCLUSIONS
The study highlights that a combination of self-reported questions can effectively identify patients with RHV, providing a feasible alternative to direct vision assessments in resource-limited settings. Implementing this screening tool could improve patient care by enabling timely adaptations and referrals for eye care, ultimately enhancing rehabilitation outcomes and reducing falls risk. Further research is needed to refine the tool's sensitivity and explore its applicability in broader hospital and primary care settings.
Early Axial Spondyloarthritis Detection
Authors: Hellamand Pasoon , van de Sande Marleen G.H. , van Bentum Rianne E. , Verbraak Frank D. , Twisk Jos W.R. , van der Horst Bruinsma Irene 
Published: February 2025

Objective
In the previous Spondyloarthritis EYE study, we confirmed the potential of a screening strategy for early axial spondyloarthritis (axSpA) detection using acute anterior uveitis (AAU) and chronic back pain (CBP) as referral criteria. This follow-up study assessed changes in diagnostic categories (definite, suspected, and no axSpA) over 2 years and identified baseline factors predicting axSpA diagnosis at 24 months.

Methods
Patients with AAU and CBP were categorized into 3 groups: definite axSpA, suspected of axSpA, and no axSpA, based on clinical and radiographic data within 6 months after baseline. Suspected cases were monitored for 24 months, with the possibility of reclassification. A competing risk analysis was used to estimate the probability of transitioning from “suspected of axSpA” to “definite axSpA” or “no axSpA,” and logistic regression analysis was employed to determine if baseline factors could predict definite axSpA at 24 months.

Results
Among 81 patients, 26 were classified as no axSpA, 36 as suspected of axSpA, and 19 as definite axSpA. At 24 months, suspected patients had an 18% probability to transition to definite axSpA (4 cases) and a 60% to no axSpA (15 cases). Significant predictors of axSpA diagnosis included the following: HLA-B27 positivity, good response to nonsteroidal anti-inflammatory drugs, inflammatory back pain, increasing C-reactive protein levels, buttock pain, and higher Bath Ankylosing Spondylitis Metrology Index scores.

Conclusions
Our screening strategy identified approximately one third of previously undiagnosed axSpA cases among patients with AAU and CBP, mostly at baseline, with few additional cases at follow-up. The predictors revealed in this study could aid physicians in estimating axSpA disease probability.
A Prediction Nomogram for Long-Term Facial Nerve Function Following Large Vestibular Schwannoma Resection
Authors: Guan Haonan , Yu Aiping , Shi Zhifeng , Wang Daohe , Ding Wei 
Published: February 2025

Objective:
The purpose of this study was to generate a nomogram for predicting long-term facial nerve (FN) function at 3 months following large vestibular schwannoma (VS) resection.

Materials and Methods:
Retrospective data were evaluated from patients who underwent VS resection from May 2014 to May 2023 at Huashan Hospital. The nomogram was conducted based on the results of univariate and multivariate logistic regression analysis of the risk factors for poor long-term FN function after VS resection.

Results:
A total of 166 cases were finally included in this study. The univariate and multivariate logistic regression analysis showed that tumor size [P=0.022, odds ratio (OR): 1.11, 95% CI: 1.02–1.22), intraoperative stimulation threshold (ST) (P=0.005, OR: 12.17, 95% CI: 2.10–70.68), tumor type (P=0.009, OR: 7.46, 95% CI: 1.64–33.86) and 3-month postoperative HB grade (P=0.005, OR: 0.883, 95% CI: 0.062–12.61) were independent risk factors for poor long-term FN function. A nomogram was conducted based on these indicators, which demonstrated good discrimination and favorable calibration.

Conclusion:
A nomogram based on 4 indicators was conducted to predict long-term FN function at 3 months following large VS resection. Patients presented with little chance of long-term FN recovery are candidates for early intervention.
Metabolomic profiling and chemical marker identification in medicinal plants of Atractylodes
Authors: Zhang Chengcai , Wang Sheng , Li Qi , Zhang Yan , He Yali , Yan Binbin , Zhou Li , Guo Lanping 
Published: February 2025

Abstract

Background
The genus Atractylodes, native to East Asia, encompasses several species that serve as sources for the widely used traditional Chinese medicines Atractylodis Macrocephalae Rhizoma and Atractylodis Rhizoma. However, the international trade arouses concern regarding potential confusion and misidentification of Atractylodes species.

Objective
A comprehensive understanding of the chemical diversity is crucial for ensuring the quality and exploring the potential variations in medicinal efficacy of Atractylodes.

Methods
The GC/MS-MS-based metabolomics and multivariate statistical analysis identified 589 differentially accumulated metabolites across 5 Atractylodes species.

Results
A total of 150 metabolites were predicted as potential chemical markers for species differentiation and quality assessment of Atractylodes. According to the metabolic profiles, the species of Atractylodes can be roughly classified into three categories: A. lancea and A. coreana with the volatile oil components being mainly atractylodin and β-eudesmol; A. macrocephala with the biomarker being atractylon; and A. japonica and A. carlinoides lying between the two categories above.

Conclusions
Metabolomic results indicated that the metabolic profiles of A. carlinoides and A. macrocephala were similar and distinct from those of the other three species. Sesquiterpenoids were the main chemical components in the rhizome of A. carlinoides, which indicated the potential medicinal value of this plant.
Learning universal knowledge graph embedding for predicting biomedical pairwise interactions
Authors: Tao Siyu , Yang Yang , Liu Xin , Feng Yimiao , Zheng Jie 
Published: February 2025

AbstractPredicting biomedical interactions is crucial for understanding various biological processes and drug discovery. Graph neural networks (GNNs) are promising in identifying novel interactions when extensive labeled data are available. However, labeling biomedical interactions is often time-consuming and labor-intensive, resulting in low-data scenarios. Furthermore, distribution shifts between training and test data in real-world applications pose a challenge to the generalizability of GNN models. Recent studies suggest that pre-training GNN models with self-supervised learning on unlabeled data can enhance their performance in predicting biomedical interactions. Here, we propose LukePi, a novel self-supervised pre-training frame-work that pre-trains GNN models on biomedical knowledge graphs (BKGs). LukePi is trained with two self-supervised tasks: topology-based node degree classification and semantics-based edge recovery. The former is to predict the degree of a node from its topological context and the latter is to infer both type and existence of a candidate edge by learning semantic information in the BKG. By integrating the two complementary tasks, LukePi effectively captures the rich information from the BKG, thereby enhancing the quality of node representations. We evaluate the performance of LukePi on two critical link prediction tasks: predicting synthetic lethality and drug-target interactions, using four benchmark datasets. In both distribution-shift and low-data scenarios, LukePi significantly outperforms 15 baseline models, demonstrating the power of the graph pre-training strategy when labeled data are sparse.
Coral venom and toxins as protection against crown-of-thorns sea star attack
Authors: Gorman Lucy M. , Huffmyer Ariana S. , Byrne Maria , Mills Suzanne C. , Putnam Hollie M. 
Published: February 2025

AbstractCrown-of-thorns sea star (CoTS) outbreaks are one of the leading causes of hard coral cover decline across the Indo-Pacific, posing a major threat to the health and resilience of coral reefs. However, the drivers underlying feeding on preferred (e.g.,Acroporaspp.) versus non-preferred (e.g.,Poritesspp.) are poorly understood. We hypothesised that coral venom may influence CoTS food preferences. We investigated whether coral venom toxin and peptide families may drive CoTS prey preferences by comparing the genomes and transcriptomes of preferred (fiveAcroporaspecies) and non-preferred (fivePoritesspecies andEchinopora lamellosa) prey species of CoTS. We constructed databases of known cnidarian venom toxins, and along with the full UniProtKB/Swiss-Prot Tox-Prot database, used these to identify toxin peptides and investigate function and phylogeny. The most abundant toxins across all coral species included kunitz-type neurotoxins, neurotoxic turripeptides, snake venom lectins, toxic proteases and actinoporins. There were proteins present only in certainPoritesspecies but completely absent from allAcroporaspecies (e.g., tereporin/conoporin, snake venom peptides) andvice versa(e.g., sarafotoxin). Further,Poritesspecies contained a homolog to conkunitzin, a toxin known to disintegrate the tube feet of CoTS, suggesting a potential mechanism for their lower susceptibility to predation. We also observed a greater diversity of jellyfish-like proteins in CoTS-exposedPoritesspecies compared to naïvePoritesspecies, suggesting these proteins deter CoTS. These findings have direct applications to assessing reef coral’s susceptibility to future CoTS outbreaks and active reef management.
A repressor co-regulatory network integrates iron acquisition to mycobacterial stress tolerance
Authors: Mehta Khushboo , Kajal  , Goar Harsh , Bamniya Bhanwar , Sarkar Dibyendu 
Published: February 2025

AbstractGrowing evidence suggests that controlled regulation of iron (Fe) uptake is essential for mycobacterial survival and proliferation in the host. In this study, we discovered the mechanism that links mycobacterial Fe acquisition to intra-bacterial redox environment via thephoPlocus. Remarkably, regulated expression of the major Fe storage protein encoding genebfrBdetermines bacterial tolerance to oxidative stress and intracellular survival of the pathogen. Transcriptomic analysis coupled within vivoDNA binding studies uncover a distinct IdeR-independent regulation, which utilizes Lsr2 and virulence regulator PhoP to modulate transcriptional control ofbfrBvia recruitment of both the regulators. A striking inhibition of Lsr2 binding to thebfrBpromoter in aphoP-KO mutant, attributable to Lsr2-PhoP protein-protein interaction, provides the most fundamental biological insight. Building on these results, we proposed a model suggesting how Lsr2-PhoP interaction (or lack thereof) contributes to repression and/or stress-specific activation ofbfrBexpression. Collectively, these results uncover a key mechanism linking Fe acquisition and oxidative stress response of mycobacteria, and have significant implications on the intracellular survival of the pathogen.
Neither exogenous, nor endogenous: evidence for a distinct role of negative emotion during attentional control
Authors: Xue Xiaojuan , Pourtois Gilles 
Published: February 2025

AbstractNegative or threatening stimuli capture attention. However, it remains unclear whether this phenomenon is best conceived as bottom-up (i.e. salience-driven) or top-down (i.e. goal- directed) instead. To address this question, we conducted two experiments using a previously validated dot-probe task (DPT) where physical salience (i.e. abrupt luminance change) and negative emotion (i.e. fearful face) competed with one another for attention selection (Experiment 1, n = 40) or negative (but also positive) emotion could be used as an endogenous cue by the participants to guide this process (Experiment 2, n = 39). Eye-tracking was used to ascertain that both cue and target were processed with peripheral vision. In Experiment 1, we found that negative emotion and physical salience both drove spatial attention in a bottom-up manner, yet their effects were under-additive, suggesting that they could mutually inhibit each other. Moreover, the results of Experiment 2 showed that fear, unlike happiness, could bias spatial attention in a top-down manner, yet only when participants were aware of the association created between the emotional cue and target’s location at the block level. Combined together, these novel findings suggest that negative value does not influence the priority map independently from physical salience and goal but depending on the specific combination of cues available for attention selection in the environment, it acts either as an exogenous or endogenous cue, thereby revealing an enhanced flexibility for it.
HKU5 bat merbecoviruses use divergent mechanisms to engage bat and mink ACE2 as entry receptors
Authors: Alfajaro Mia Madel , Keeler Emma L. , Li Ning , Catanzaro Nicholas J. , Teng I-Ting , Zhao Zhe , Grunst Michael W. , Yount Boyd , Schäfer Alexandra , Wang Danyi , Kim Arthur S. , Synowiec Aleksandra , Peña-Hernández Mario A. , Arinola Ridwan , Kaur Ramandeep , Menasche Bridget L. , Wei Jin , Russell Gabriel A. , Huck John , Song Jaewon , Ring Aaron , Iwasaki Akiko , Jangra Rohit K. , Lee Sanghyun , Martinez David R. , Mothes Walther , Uchil Pradeep D. , Doench John G. , Spaulding Alicen B. , Baric Ralph S. , Serebryannyy Leonid , Tsybovsky Yaroslav , Zhou Tongqing , Douek Daniel C. , Wilen Craig B. 
Published: February 2025

AbstractIdentifying receptors for bat coronaviruses is critical for spillover risk assessment, countermeasure development, and pandemic preparedness. While Middle East respiratory syndrome coronavirus (MERS-CoV) uses DPP4 for entry, the receptors of many MERS-related betacoronaviruses remain unknown. The bat merbecovirus HKU5 was previously shown to have an entry restriction in human cells. Using both pseudotyped and full-length virus, we show that HKU5 usesPipistrellus abramusbat ACE2 but not human ACE2 or DPP4 as a receptor. Cryo-electron microscopy (cryo-EM) analysis of the virus-receptor complex and structure-guided mutagenesis reveal a spike and ACE2 interaction that is distinct from other ACE2-using coronaviruses. MERS-CoV vaccine sera poorly neutralize HKU5 informing pan-merbecovirus vaccine design. Notably, HKU5 can also engage American mink and stoat ACE2, revealing mustelids as potential intermediate hosts. These findings highlight the versatility of merbecovirus receptor use and underscore the need for continued surveillance of bat and mustelid species.
Mobile genetic elements that shape microbial diversity and functions in thawing permafrost soils
Authors: Guo Jiarong , Aroney Samuel , Dominguez-Huerta Guillermo , Smith Derek , Vik Dean , Ansah Carlos Owusu , Pratama Akbar Adjie , Solonenko Sergei , Tian Funing , Howard-Varona Cristina , Zhong ZhiPing , Fofana Aminata , Smith Garrett , Hodgkins Suzanne B. , Cronin Dylan ,   EMERGE Field Teams 2010-2019,   EMERGE Coordinators, Woodcroft Ben J. , Tyson Gene W. , Rich Virginia I. , Sullivan Matthew B. , Roux Simon , Bagby Sarah C. 
Published: February 2025

AbstractMicrobiomes shape ecosystems through functional profiles influenced by gene gains and losses. While culture-based experiments demonstrate that mobile genetic elements (MGEs) can mediate gene flux, quantitative field data remains scarce. Here we leverage large-scale soil meta-omic data to develop and apply analytics for studying MGEs. In our model permafrost-thaw ecosystem, Stordalen Mire, we identify ∼2.1 million MGE recombinases across 89 microbial phyla to assess ecological distributions, functions impacted, and past mobility and current activity. This revealed MGEs shape natural genetic diversity via lineage-specific engagement, and functions including canonical defense elements alongside diverse regulatory and metabolic genes affecting carbon flux and nutrient cycling. These findings and this systematic meta-omic framework open new avenues to better investigate MGE diversity, activity, mobility, and impacts in nature.One Sentence SummaryBy developing microbiome-ready analytics and applying them to thawing permafrost microbiomes, we identified ∼2.1 million diverse mobile genetic element (MGE) recombinases (integrons, insertion sequences, transposons, conjugative elements, phage-like elements) and revealed their function and activity to establish baseline ecological data and a framework for MGE study in complex natural systems.
Dynamic regulation of Sec24C by phosphorylation and O-GlcNAcylation during cell cycle progression
Authors: Georgiou George R. , Hirata Tetsuya , Soderblom Erik , Homoelle Rose , Maiwald Jakob , Boyce Michael 
Published: February 2025

AbstractDuring mitosis, eukaryotic cells cease anterograde trafficking from the endoplasmic reticulum (ER) towards the Golgi. This cessation corresponds with the dispersal of the COPII transport protein, Sec24C, from juxtanuclear ER exit sites (ERES) into a diffusely cytosolic pool. Redistribution of Sec24 paralogs and other core COPII proteins may underlie the mitotic pause in secretion and may be required for the equal inheritance of endomembrane organelles and machinery by both daughter cells. Therefore, it is important to understand the mechanisms governing the mitotic relocalization of COPII components. Here, we explore the role of post-translational modifications (PTMs) of the model COPII protein Sec24C in this phenotypic switch during mitosis. In interphase, Sec24C is modified by O-linked β-N-acetylglucosamine (O-GlcNAc), and we show that this glycan is rapidly removed upon mitotic entry, influencing the timing of Sec24C dispersal. Additionally, we identify novel, cell cycle phase-enriched phosphorylation events on Sec24C, including phosphosites that regulate the stability and localization of the protein, providing the first systematic characterization of dynamic PTMs on any Sec24 protein. Together, our data support the hypothesis that phosphorylation and glycosylation of Sec24C act in concert to induce rapid dispersal upon mitotic entry and may promote equal partitioning of the endomembrane system to daughter cells after division.
Assessing the Accuracy of CGM Metrics: The Role of Missing Data and Imputation Strategies
Authors: Cichosz Simon Lebech , Kronborg Thomas , Hangaard Stine , Vestergaard Peter , Jensen Morten Hasselstrøm 
Published: February 2025

AbstractAimThis study aims to evaluate the accuracy of continuous glucose monitoring (CGM)-derived metrics, particularly those related to glycemic variability, in the presence of missing data. It systematically examines the effects of different missing data patterns and imputation strategies on both standard glycemic metrics and complex variability metrics.MethodsThe analysis modeled and compared the effects of three types of missing data patterns—missing completely at random (MCAR), segmental gaps, and blockwise gaps—with proportions ranging from 5% to 50% on CGM metrics derived from 14-day profiles of individuals with type 1 and type 2 diabetes. Six imputation strategies were assessed: data removal, linear interpolation, mean imputation, piecewise cubic Hermite interpolation, temporal alignment imputation (TAI) and random forest-based imputation.ResultsA total of 933 14-day CGM profiles from 468 individuals with diabeteswere analyzed. Across all metrics, the coefficient of determination (R2) improved as the proportion of missing data decreased, regardless of the missing data pattern. The impact of missing data on the agreement between imputed and reference metrics varied depending on the missing data pattern. To achieve high accuracy (R2> 0.95) in representing true metrics, at least 80% of the CGM data was required. While no imputation strategy fully compensated for high levels of missing data, simple removal and TAI outperformed others in certain scenarios.ConclusionThis study highlights the significant impact of missing data and imputation strategies on CGM-derived metrics, particularly glycemic variability and time below range (TBR) estimates. The findings underscore the necessity of rigorous data handling practices to ensure reliable assessments of glycemic control and variability.
Prevalence, Risk Factors, Hesitancy, and Attitudes Toward Vaccination Against Reproductive Tract Infections Among Women in an Urban Setting: A Cross-Sectional Survey Study
Authors: Yadav Sunita K. , Bhardwaj Priya , Kant Ravi , Ghosh Joyeta , Mangla Anita Garg , Muralidhar Sumathi , Saluja Daman , Singh Rita , Sikora Aleksandra E. , Taneja Jyoti 
Published: February 2025

AbstractBackgroundReproductive tract infections (RTIs) including sexually transmitted infections (STIs), endogenous and iatrogenic infections are a major health concern globally, particularly among young women in developing nations. If untreated, they can lead to infertility, increased HIV susceptibility, and cervical cancer. This study examines RTI symptoms prevalence, risk factors, and hesitancy toward STI vaccination.MethodsA cross-sectional study was conducted among 1,920 urban women (predominantly aged 18-25) in Delhi/NCR using a structured questionnaire. Data on demographics, reproductive health, RTI symptoms, and vaccine awareness were analyzed using SPSS 20. Chi-square tests, Fisher’s exact tests, and Bonferroni corrections were applied, with multinomial logistic regression identifying RTI risk predictors.ResultsAmong respondents, 1,240 (64.6%) reported RTI symptoms, with 1,029 (83%) experiencing vaginal discharge and 974 (78.5%) vulval itching. Significant risk factors included early menarche, irregular menstrual cycles, poor menstrual hygiene, and prior RTI medication use. Additionally, 1,033 (53.8%) were hesitant about STI vaccination, citing safety concerns (36%, 372) and cost (18.6%, 192). However, 826 (43%) reported that healthcare provider recommendations positively influenced their decision to vaccinate.ConclusionThe high prevalence of RTI symptoms highlights the urgent need for improved awareness, accessible healthcare services, and stronger vaccination promotion efforts to enhance RTI prevention and management.