bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clinical relevance of current patient-reported outcome measures for ankle fracture: surgeons' perspective
Authors: Schweser Kyle , Leary Emily , Levack Ashley E. , Marmor Meir T. ,   members of the OTA Classification and Outcomes Committee,   OTA Evidence Based Quality, Value and Safety Committee
Published: October 2024

Abstract

Objectives:
Determine the relevance of the most frequently used patient-reported outcome measures (PROMs) for monitoring patient recovery after ankle fracture, from the clinical perspective of orthopaedic trauma surgeons, given lack of validated PROMs.

Design:
Prospective cohort.

Setting:
Orthopaedic Trauma Association committee meetings, electronic correspondence.

Patients/Participants:
Orthopaedic trauma surgeons.

Intervention:
Delphi method for consensus activities.

Level of Evidence:
IV.

Main Outcome Measurements:
Most clinically relevant PROMs for ankle fracture recovery.

Results:
Several English-language PROMs were identified based on use in literature and relevance to ankle fractures. 7 were selected by expert consensus. These are the Ankle Fracture Outcome of Rehabilitation Measure (A-FORM), Foot and Ankle Ability Measure (FAAM), American Academy of Orthopaedic Surgeons (AAOS), Foot and Ankle Disability Index (FADI) Score, Lower Extremity Functional Scale (LEFS), Olerud–Molander Ankle Score (OMAS), and Patient-Reported Outcome Measurement Information System Physical Function (PROMIS PF). The most clinically relevant PROM is the A-FORM, followed by the AAOS, LEFS, PROMIS PF, FADI, and OMAS, and the least clinically relevant overall, the FAAM.

Conclusions:
Understanding which PROM best matches physician expectations for tracking recovery is an important step toward a robust, evidence-based approach to patient care. The A-FORM was identified as the most clinically relevant among the most used PROMs. These results will aid surgeons, clinicians, and scientists to identify a uniformly, clinically relevant PROM for the treatment and study of outcomes and recovery after isolated ankle fracture.
Adaptive behavior in response to the 2022 mpox epidemic in the Paris region
Authors: Maniscalco Davide , Robineau Olivier , Boëlle Pierre-Yves , Mazzoli Mattia , Barret Anne-Sophie , Chazelle Emilie , Mailles Alexandra , Noël Harold , Tarantola Arnaud , Velter Annie , Zanetti Laura , Colizza Vittoria 
Published: October 2024

ABSTRACTThe 2022 mpox outbreak saw a rapid case surge among men-who-have-sex-with-men (MSM) in previously unaffected regions, driven by heterogeneity in sexual networks. A sudden decline followed, but its drivers remain unclear as it is difficult to distinguish the roles of vaccination, herd immunity, and behavioral changes. We developed a network model of mpox transmission among MSM based on sexual behavior data and fitted it to the Paris region epidemic. We studied whether the decline was driven by post-exposure prophylaxis (PEP) vaccination, immunity among highly active MSM, or behavioral changes. Behavioral shifts were modeled as either uniform or based on individual risk factors, like sexual activity or exposure to diagnosed cases. We used the cross-sectional 2023 ERAS survey to validate findings. Behavioral changes adopted by 49% (95%CI 47-51%) of MSM regardless of individual risk factors best explained the observed epidemic decline. These changes prevented an estimated 73% (28-99%) of mpox cases in summer 2022. Findings aligned with the ERAS survey data, showing that 46% (45-48%) of MSM reduced sexual partners. On the contrary, PEP vaccination and immunity among highly active MSM were insufficient to curb the outbreak. Widespread behavioral change was the primary driver of the mpox epidemic decline in the Paris region, before preventive vaccination or immunity could affect epidemic spread. These findings highlight the importance of effective risk communication and community engagement in outbreak management. Tailored public health responses that encourage adaptive behaviors, especially as vaccination efforts ramp up, are essential for supporting affected communities.
DNA methylation stochasticity is linked to transcriptional variability and identifies convergent epigenetic disruption across genetically-defined subtypes of AML
Authors: Hilgart Eleanor , Zhou Weiqiang , Martinez-Montes Eduardo , Idrizi Adrian , Tryggvadottir Rakel , Gondek Lukasz P. , Majeti Ravindra , Ji Hongkai , Koldobskiy Michael A. , Feinberg Andrew P. 
Published: October 2024

AbstractDisruption of the epigenetic landscape is of particular interest in acute myeloid leukemia (AML) due to its relatively low mutational burden and frequent occurrence of mutations in epigenetic regulators. Here, we applied an information-theoretic analysis of methylation potential energy landscapes, capturing changes in mean methylation level and methylation entropy, to comprehensively analyze DNA methylation stochasticity in subtypes of AML defined by mutually exclusive genetic mutations. We identified AML subtypes with CEBPA double mutation and those with IDH mutations as distinctly high-entropy subtypes, marked by methylation disruption over a convergent set of genes. We found a core program of epigenetic landscape disruption across all AML subtypes, with discordant methylation stochasticity and transcriptional dysregulation converging on functionally important leukemic signatures, suggesting a genotype-independent role of stochastic disruption of the epigenetic landscape in mediating leukemogenesis. We further established a relationship between methylation entropy and gene expression variability, connecting the disruption of the epigenetic landscape to transcription in AML. This approach identified a convergent program of epigenetic dysregulation in leukemia, clarifying the contribution of specific genetic mutations to stochastic disruption of the epigenetic and transcriptional landscapes of AML.
Exploring The Genome of The Oribatid Mite,Oppia Nitens– Environmental Stress Response and Toxicity Adaptation
Authors: Adedokun Adedamola A. , Fajana Hamzat O. , Jegede Olukayode O. , Hammond Austin S. , Smith Derek D.N. , Kvas Stephanie , Hewavithana Thulani , Jin Lingling , Princz Juliska , Siciliano Steven D. 
Published: October 2024

AbstractOribatid mites are one of the most abundant groups of microarthropods in soil.Oppia nitens, belonging to the family Oppiidae, one of the largest and most diverse families of oribatid mites, has been developed as a standardized model test organism for assessing soil contamination. However, the limited availability of genomic information for this species hinders our understanding of its physiological adaptation and sensitivity to chemical and environmental stressors in soil. Hence, we present the annotatedO. nitensdraft genome assembled using both Oxford Nanopore Technologies and Illumina sequencing platforms as a basis to identify potential genes that can be linked to adaptation to chemical and environmental stressors.The sequences were assembled into 65 scaffolds spanning 125.4Mb with a 24.5% GC content and an N50 length of 4.41Mb. Genome quality and completeness were checked using arthropod Benchmarking Universal Single-Copy Orthologs (BUSCO) analysis, which identified 93.5 % complete single-copy orthologs, 3.4% complete but duplicated orthologs, 0.5% fragmented, and 2.6% missing orthologs (n=2934). The NCBI Eukaryotic Genome Annotation Pipeline annotated 15,291 genes, 16,969 mRNAs, and 14,938 proteins.Here, we describe theO. nitenscomplete draft genome and discuss its utility as a genetic basis for further investigations and understanding of the molecular mechanisms and physiological functions in adaptations to environmental change, especially tolerance to metal stress.
Intracellular amphiregulin is critical for heterochromatin maintenance and genomic stability in response to replication stress inBRCA2mut/+mammary epithelial cells
Authors: Jiang Tianqi , Zein Aiman , Christine Pratt M.A. 
Published: October 2024

AbstractThe BRCA2 tumor suppressor protein has roles in homologous recombination DNA repair and replication fork protection and carriers of mutation in theBRCA2gene (BRCA2mut/+) are at high risk for breast cancers as a consequence of genomic instability. Mammary epithelial cells (MECs) are subjected to significant hormone-driven replication.BRCA2mut/+MECs must therefore be able to mitigate RS-induced chronic DNA damage that could result in cell death or senescence. In response to acute RS in hTERT-MECs, we have found that the EGFR ligand, amphiregulin (AREG) rapidly undergoes retrograde trafficking to the nucleus and nuclear membrane (NM) in association with lamin A resulting in a transient increase in H3K9me3 heterochromatin most markedly inBRCA2mut/+hTERT-MECs. RS promoted NM incorporation of prelamin A that was dependent on endogenous but not exogenous AREG. Prelamin A is reported to stabilize SUV39h1 and expression of a C-terminal truncated AREG that translocates to the NM increased SUV39h1, HP1α and H3K9me3. AREG knockdown reduced both HP1α and SUV39h1 accompanied by massive decompaction and reduction in global H3K9me3 heterochromatin. Loss of heterochromatin upon AREG depletion increased DNA damage, reduced replication fork speed and resulted in a significant increase in firing of new and multiple origins. Knockdown of endogenous AREG also impacted the NM resulting in activation of a type-1 interferon (IFN)-like response promoting senescence. Chronic RS also stimulated nuclear AREG along withFOXM1andESR1mRNA and protein. Consistent with this, nuclear AREG, FOXM1 and ERα were detected in hyperplastic regions of human tissue. Overall, our work reveals a critical and unanticipated nuclear role for AREG in maintenance and transient induction of heterochromatin in response to RS preventing excessive DNA damage and senescence inBRCA2mut/+MECs. Since nuclear AREG also promotes ERα expression, this may link RS with aberrant expansion of estrogen receptor-expressing MECs found inBRCA2mut/+mammary tissue.
GenePert: Leveraging GenePT Embeddings for Gene Perturbation Prediction
Authors: Chen Yiqun , Zou James 
Published: October 2024

AbstractPredicting how perturbation of a target gene affects the expression of other genes is a critical component of understanding cell biology. This is a challenging prediction problem as the model must capture complex gene-gene relationships and the output is high-dimensional and sparse. To address this challenge, we present GenePert, a simple approach that leverages GenePT embeddings, which are derived using ChatGPT from text descriptions of individual genes, to predict gene expression changes due to perturbations via regularized regression models. Benchmarked on eight CRISPR perturbation screen datasets across multiple cell types and five different pretrained gene embedding models, GenePert consistently outperforms all the state-of-the-art prediction models measured in both Pearson correlation and mean squared error metrics. Even with limited training data, our model generalizes effectively, offering a scalable solution for predicting perturbation outcomes. These findings underscore the power of informative gene embeddings in predicting the outcomes of unseen genetic perturbation experimentsin silico. GenePert is available athttps://github.com/zou-group/GenePert.
Intra-arterial Deoxyribonuclease therapy improves stroke outcomes in aged mice
Authors: Yin Junxiang , Wu Michael , White Jennifer , StClair Ellie , Waters Michael F. 
Published: October 2024

AbstractBackgroundFutile recanalization affects more than half of acute ischemic stroke (AIS) patients. Neutrophil extracellular traps (NETs) are a major factor of microvascular hypoperfusion after stroke. Deoxyribonuclease I (DNase) targeting NETs exhibited a neuroprotective effect in young mice with AIS. This study explored a novel direct intra-arterial administration of DNase therapy and its effect in aged mice with AIS.MethodAIS was induced in aged C57BL/6 mice followed by reperfusion and immediate, intra-arterial DNase administration via the internal carotid artery. Cerebral blood flow, neurological function, cerebral infarct volume, and NET markers were examined.ResultsDirect intra-arterial DNase therapy significantly increased cerebral blood flow, reduced neurological deficit scores, increased the latency to fall in wire hang test, reduced cerebral infarct volume, and decreased neutrophil and NET count in both the parenchyma and micro vessels in aged mice with AIS compared with age-matched, vehicle controls.ConclusionOur data is the first to demonstrate that successful, direct intra-arterial DNase therapy provides more efficient cerebral reperfusion and better outcomes after recanalization during the treatment of large vessel occlusion in aged mice. This study provides evidence for the potential clinical application of catheter delivered intra-arterial DNase therapy post-recanalization.
eIF4ET regulates meiotic proteome levels to enable oocyte formation and storage
Authors: Bhatia Priyankaa , Amin Ruchi , Familiari Nicole E. , Yaguchi Kan , Tran Vanna M. , Bond Alec , Bukulmez Orhan , Woodruff Jeffrey B. 
Published: October 2024

ABSTRACTAnimals store oocytes in a dormant state for weeks to decades before ovulation. The homeostatic programs oocytes use to endure long-term storage are poorly understood. Using female nematodes as a short-lived model, we found that oocyte formation and storage required IFET-1, the conserved eIF4E-Transporter protein (eIF4ET). IFET-1 co-assembled with CAR-1 (Lsm14) to form micron-scale condensates in stored oocytes, which dissipated after oocyte activation. Depletion of IFET-1 destabilized the oocyte proteome, leading to a decline in microtubule maintenance proteins and errors in microtubule organization and meiotic spindle assembly. Deleting individual domains within IFET-1 impaired oocyte storage without affecting oocyte formation. Thus, in addition to establishing a healthy oocyte reserve in young mothers, IFET-1 ensures that correct levels of cytoskeletal proteins are maintained as oocytes age. Human eIF4ET also localized to micron-scale puncta in dormant oocytes in a reproductively healthy patient. Our results identify a role for eIF4ET in maintaining the oocyte reserve and implicate eIF4ET dysfunction as an upstream cause of embryonic aneuploidy and age-related infertility.
SCAD Delivery Platform: A Novel Approach for Efficient CNS and Extrahepatic Oligonucleotide Therapeutics
Authors: Kang Moorim , Lin Wei-Hsiang , Xu Feifei , Zhou Xiaojie , Si Chunyan , Liu Kunshan , Dai Jianxiu , He Jichao , Schacht Ian , Li Yichen , Gan Zubao , Li Long-Cheng 
Published: October 2024

ABSTRACTOligonucleotide therapeutics, including antisense oligonucleotides (ASOs) and duplex RNAs like siRNA, saRNA, and miRNA, hold immense potential for treating genetic and acquired diseases by modulating gene expression in a target-specific manner. However, effective delivery to extrahepatic tissues, particularly the central nervous system (CNS), remains a significant challenge. While GalNAc conjugation has enabled liver-specific delivery, leading to several approved siRNA drugs for hepatic targets, CNS delivery lags. ASOs, on the other hand, can self-deliver to the CNS when administered locally, as seen with nusinersen and tofersen. To address this disparity, we’ve developed the Smart Chemistry Aided Delivery (SCAD) platform which enables duplex RNA delivery by conjugating it to an accessory oligonucleotide (ACO), which acts as an aptamer to mediate protein binding and facilitate cellular uptake. Through extensive screening, we identified an optimal SCAD architecture that demonstrates enhanced cell-free protein binding andin vitroactivity. In rodent models, local administration of SCAD-siRNA conjugates resulted in broad biodistribution throughout the CNS and sustained mRNA knockdown for over five months, with a favorable safety profile. The SCAD platform also exhibited efficient delivery to other tissues, including the eye, the lung and the joint. These features support its potential for broader clinical applications, as evidenced by an ongoing trial targeting amyotrophic lateral sclerosis (ALS) associated with mutations in theSOD1gene. The modular design of SCAD allows it to easily adapt to any duplex RNA, making it a powerful tool for advancing oligonucleotide therapeutics.
Ictal-Related Chirp as a Biomarker for Monitoring Seizure Progression
Authors: Bahador Nooshin , Skinner Frances , Zhang Liang , Lankarany Milad 
Published: October 2024

AbstractDespite being prevalent, the causes, mechanisms, and progression of epilepsy—a chronic neurological disorder with unprovoked seizures—are not well understood, complicating drug development for treatment. This study used a comprehensive mouse epilepsy kindling model dataset to investigate frequency modulation (chirp) as a potential indicator of distinct states of epilepsy (early evoked discharge, late evoked discharge, spontaneous recurrent seizure, and drug state). Employing time-frequency ridge extraction, chirp identification, and statistical testing, our analyses revealed that chirp patterns occur in the majority of ictal discharges (>81.6%), persisting across evoked and spontaneous seizures. While the focus was on hippocampal recordings, chirps were also detected in the piriform peripheral cortex. Significant frequency and duration changes in chirp patterns during the transition from early to late evoked ictal events suggest their potential as the screening tool for seizure progression. Additionally, detailed analyses illuminate the impact of Lorazepam, aGABAAenhancer, on chirp characteristics, providing insights into how increased inhibitory tone quantifiably influences excitatory-inhibitory balances during seizures.
Analysis of off-momentum nonlinear driving terms for enlarging off-momentum dynamic apertures
Authors: Wei Bingfeng , Bai Zhenghe , Feng Guangyao , Loulergue Alexandre , Nadolski Laurent S. , Nagaoka Ryutaro 
Published: October 2024

Due to scattering, particles in a ring may have large momentum deviations, which will change their dynamics, potentially resulting in particle losses. Optimization of off-momentum nonlinear dynamics is, therefore, important for increasing beam lifetime. When analyzing off-momentum dynamics using the approach of resonance driving terms (RDTs), chromatic RDTs are usually used, which denote the deviations from on-momentum dynamics. In this paper, instead of using chromatic RDTs, we propose using off-momentum RDTs to analyze off-momentum dynamics, which is a more direct way. As in the case of on-momentum dynamics, the nonlinear driving terms for off-momentum particles include off-momentum RDTs and off-momentum amplitude-dependent tune shifts, which are calculated based on off-momentum linear optics. Similar to the analysis of on-momentum dynamics in our previous work [B. Wei , ], we study the fluctuation or variation of off-momentum RDTs along the longitudinal position, which is very effective for analyzing and optimizing off-momentum dynamic apertures (DAs). Similar results are obtained for the off-momentum case: (i) minimizing the element-by-element average of the RDTs is more effective than minimizing one-turn RDTs in enlarging DAs and (ii) minimizing the average of lower-order RDTs helps reduce higher-order RDTs.

Published by the American Physical Society
2024
Leadership styles and collection development practices of librarians in academic libraries: a case of Ekiti state, Nigeria
Authors: Oguntuase Moyosade Omolade , Okhakhu David O. , Fasae Joseph Kehinde 
Published: October 2024

Purpose
The purpose of this study was to investigate the impact of leadership styles on collection development practices in academic libraries within Ekiti State, Nigeria.

Design/methodology/approach
The research used a survey research design, using a questionnaire as the primary data collection instrument. The study encompassed 86 library personnel selected from six academic libraries in Ekiti State.

Findings
The study’s findings revealed a notably high level of engagement in collection development practices within the academic libraries under investigation. In addition, the library managers exhibited a blend of leadership styles, with the democratic style being the most frequently used, followed by autocratic and laissez-faire styles. Furthermore, the research identified a significant influence of leadership styles on collection development practices, with evidence suggesting a collective impact when considering various leadership styles together.

Social implications
The study implies that effective leadership plays a crucial role in realizing the overarching objectives of academic libraries, and a well-informed leadership approach positively impacts the library’s ability to meet its collection development goals and serve its academic community effectively.

Originality/value
This study contributes to the existing body of knowledge by shedding light on the intricate relationship between leadership styles and collection development practices in academic libraries. The identification of a predominant democratic leadership style and its implications on library practices provides a nuanced understanding of leadership dynamics in this context.
Consumerbased conceptualisation of brand transparency: scope, characteristics and contextual determinants
Authors: Sansome Kate , Conduit Jodie , Wilkie Dean Charles Hugh 
Published: October 2024

Purpose
Escalating uncertainty surrounding brand communications has intensified consumer demands for transparency. Many definitions link transparency to the quantity of shared information, yet more information might not alleviate consumer uncertainty. The purpose of this paper is to develop a consumer-based conceptualisation of brand transparency that recognises the subjectivity in how transparency manifests for consumers.

Design/methodology/approach
This research adopts a qualitative approach, leveraging 10 exploratory interviews with experts and 20 in-depth interviews with consumers.

Findings
Confronted with information asymmetry, consumers rely on cues (openness, clarity, timeliness, evidence-based, explanatory) to evaluate a brand’s intentions to provide accurate information about focal domains in a way that establishes brand transparency. Focal domains of brand transparency (pro-social values, processes and product and service offerings) evolve in line with changing consumer expectations. Both consumer relationships and brand experiences influence brand transparency perceptions.

Research limitations/implications
This study challenges an inherent assumption that access to more information informs brand transparency perceptions; instead, consumers require transparency about salient and focal topics. By delineating the observable signals consumers use to infer transparency and highlighting how consumers’ biases towards certain brands and product categories influence their perceptions of brand transparency, this study contributes to customer–brand relationship literature.

Practical implications
The authors identify challenges for evoking brand transparency perceptions when information is salient. The authors stress the importance of open dialogue across all touchpoints to address consumer queries.

Originality/value
By challenging some assumptions of brand transparency literature, which have evolved from accounting and governance disciplines, this research introduces a distinctive perspective on consumer-based brand transparency.