bluuebunny/crossref_metadata_2025_split huggingface dataset:
Variety of disc wind-driven explosions in massive rotating stars – II. Dependence on the progenitor
Authors: Menegazzi Ludovica Crosato , Fujibayashi Sho , Shibata Masaru , Betranhandy Aurore , Takahashi Koh 
Published: January 2025

ABSTRACT
We assess the variance of supernova(SN)-like explosions associated with the core collapse of rotating massive stars into a black hole-accretion disc system under changes in the progenitor structure. Our model of the central engine evolves the black hole and the disc through the transfer of matter and angular momentum and includes the contribution of the disc wind. We perform two-dimensional, non-relativistic, hydrodynamics simulations using the open-source hydrodynamic code athena++, for which we develop a method to calculate self-gravity for axially symmetric density distributions. For a fixed model of the wind injection, we explore the explosion characteristics for progenitors with zero-age main-sequence masses from 9 to 40 $\mathrm{ M}_\odot$ and different degrees of rotation. Our outcomes reveal a wide range of explosion energies with $E_\mathrm{expl}$ spanning from ${\sim} 0.3\times 10^{51}$ to $\gt 8\times 10^{51}$ erg and ejecta mass $M_\mathrm{ej}$ from ${\sim} 0.6$ to ${\gt} 10 \,\mathrm{ M}_\odot$. Our results are in agreement with some range of the observational data of stripped-envelope and high-energy SNe such as broad-lined type Ic SNe, but we measure a stronger correlation between $E_\mathrm{expl}$ and $M_\mathrm{ej}$. We also provide an estimate of the $^{56}$Ni mass produced in our models which goes from ${\sim} 0.04$ to ${\sim} 1.3\, \mathrm{M}_\odot$. The $^{56}$Ni mass shows a correlation with the mass and the angular velocity of the progenitor: more massive and faster rotating progenitors tend to produce a higher amount of $^{56}$Ni. Finally, we present a criterion that allows the selection of a potential collapsar progenitor from the observed explosion energy.
Ubiquitin protease Ubp1 cooperates with Ubp10 and Ubp12 to revert lysine-164 PCNA ubiquitylation at replication forks
Authors: Zamarreño Javier , Rodríguez Sergio , Muñoz Sofía , Bueno Avelino , Sacristán María P 
Published: January 2025

Abstract
Proliferating cell nuclear antigen (PCNA) is essential for the faithful duplication of eukaryotic genomes. PCNA also orchestrates events necessary to address threats to genomic integrity, such as the DNA damage tolerance (DDT) response, a mechanism by which eukaryotic cells bypass replication-blocking lesions to maintain replisome stability. DDT is regulated by the ubiquitylation of PCNA and the consequent recruitment of specialized polymerases that ensure replication continuity. We have recently described that the deubiquitylases Ubp10 and Ubp12 modulate DDT events by reverting the ubiquitylation of PCNA in Saccharomyces cerevisiae. This study identifies Ubp1 as a novel PCNA deubiquitylase that cooperates with Ubp10 and Ubp12 in the regulation of DDT during DNA replication. Ubp1, previously known as a cytoplasmic protein, also localizes to the nucleus, where it associates with DNA replication forks. Additionally, Ubp1 interacts with and deubiquitylates PCNA. Here, we provide evidence that Ubp1 collaborates with Ubp10 and Ubp12 to facilitate DNA replication by efficiently reverting PCNAK164 ubiquitylation at replication forks under conditions free from exogenous perturbations. Consequently, the deletion of UBP1, UBP10, and UBP12 leads to persistent ubiquitylation of PCNAK164 and a marked delay in S phase progression.
Oncohistone H3 E97K mutation facilitates CENP-A mislocalization and chromosomal instability in budding yeast
Authors: Ohkuni Kentaro , Au Wei-Chun , Kazi Amira Z , Balachandra Vinutha , Basrai Munira A 
Published: January 2025

Abstract
Mislocalization of overexpressed CENP-A (Cse4 in budding yeast) contributes to chromosomal instability (CIN) in yeasts, flies, and human cells. Overexpression of CENP-A is observed in many cancers and this correlates with poor prognosis. Here, we show that altered stoichiometry of histone H3 and expression of oncohistone mutation H3 E97K contributes to mislocalization of Cse4 and CIN. Oncohistone mutations in the globular domain of histone H3 such as H3 E97K occur in several cancers; however, their functional effects remain unexplored. We demonstrated that strains with reduced gene dosage of histone H3 (hht1Δ and hht2Δ) or oncohistone H3 E97K mutation exhibit enhanced Cse4–H4 interaction, an in vivo change in the conformational state of Cse4, and this contributes to mislocalization of Cse4. Oncohistone H3 E97K mutant protein was unstable and exhibited defects in interaction with histone H4. Notably, mislocalization of Cse4 and CIN phenotypes were observed in hht1Δ and oncohistone H3 E97K mutants expressing endogenous Cse4. In summary, our studies highlight the importance of histone H3 stoichiometry in preventing mislocalization of Cse4 for chromosomal stability and suggest that oncohistone H3 mutations may contribute to CIN in human cancers.
Consistent features observed in structural probing data of eukaryotic RNAs
Authors: Yamamura Kazuteru , Asai Kiyoshi , Iwakiri Junichi 
Published: January 2025

Abstract
Understanding RNA structure is crucial for elucidating its regulatory mechanisms. With the recent commercialization of messenger RNA vaccines, the profound impact of RNA structure on stability and translation efficiency has become increasingly evident, underscoring the importance of understanding RNA structure. Chemical probing of RNA has emerged as a powerful technique for investigating RNA structure in living cells. This approach utilizes chemical probes that selectively react with accessible regions of RNA, and by measuring reactivity, the openness and potential of RNA for protein binding or base pairing can be inferred. Extensive experimental data generated using RNA chemical probing have significantly contributed to our understanding of RNA structure in cells. However, it is crucial to acknowledge potential biases in chemical probing data to ensure an accurate interpretation. In this study, we comprehensively analyzed transcriptome-scale RNA chemical probing data in eukaryotes and report common features. Notably, in all experiments, the number of bases modified in probing was small, the bases showing the top 10% reactivity well reflected the known secondary structure, bases with high reactivity were more likely to be exposed to solvent and low reactivity did not reflect solvent exposure, which is important information for the analysis of RNA chemical probing data.
Prevalence of Asymptomatic Acetabular Labrum Abnormalities in the Active Pediatric Population
Authors: Jones Hunter , Chang I-Yuan Joseph , Chen Diana , Kalia Vivek , Alizai Hamza , Wilson Philip L. , Ellis Henry B. 
Published: January 2025

Background:
The prevalence of labral tears in asymptomatic active adults has been reported, but the prevalence of labral tears and other incidental hip lesions in the asymptomatic active pediatric population remains unclear. The purpose of this study was to determine the prevalence of hip abnormalities detected on 3T MRI in an active pediatric population with no hip symptoms and to compare with hip abnormalities found in children and adolescents who underwent an MRI for a hip-related condition.

Methods:
After IRB approval, pediatric patients self-reporting as athletes and presenting with isolated, acute-onset knee pain requiring knee MRI were prospectively recruited to undergo 3T MRI of their asymptomatic contralateral hip (ASx). A comparison group of pediatric subjects who underwent an MRI for hip pain was enrolled retrospectively (Sx). All MRI scans were anonymized and randomized. Fifty subjects were enrolled for each cohort. Two fellowship-trained musculoskeletal radiologists independently evaluated MRIs for abnormal hip lesions, including labral tears. Inter-reader reliability was evaluated using Cohen Kappa. χ2 or Fisher exact test was used to compare the prevalence of hip lesions between the 2 cohorts.

Results:
The average patient age was 14.9 years for both cohorts (range 9 to 18 y) and 48% were male. In the ASx group, incidental labral tears were found in 18%, labral/paralabral cysts 6%, cartilage lesion 0%, subchondral cyst 0%, ligamentum teres tear 0%, femoral fibrocystic change 0%, cam lesion 30%, acetabular bone edema 0%, acetabular rim fracture 0%. The prevalence of labral tears (30%, P-value 0.16) and cam lesion (36%, P-value 0.52) in the Sx group was not significantly different from the ASx cohort. No significant correlation was found between the presence of femoral neck osseous bump and labral tear, labral cyst, or paralabral cyst in either cohort.

Conclusions:
Labral tears were present on 3T MRIs of active pediatric patients with and without hip pain. Although MRI is essential to confirm the surgeon’s suspicion and to detect unexpected pathology, clinical examination and history are crucial in pinpointing clinically relevant abnormal imaging findings.

Level of Evidence:
Level III.
Defining Substantial Clinical Benefits of PROMIS Pain Interference and Physical Function in Patients Undergoing Lumbar and Thoracolumbar Spine Surgery
Authors: Yakdan Salim , Frumkin Madelyn R. , Javeed Saad , Plog Benjamin A. , Zhang Justin K. , Benedict Braeden , Botterbush Kathleen , Goodin Burel R. , Piccirillo Jay F. , Buchowski Jacob M. , Rodebaugh Thomas L. , Ray Wilson Z. , Kelly Michael P. , Greenberg Jacob K. 
Published: January 2025

Study Design.
Prospective cohort study.

Objective.
This study aims to define Substantial Clinical Benefit (SCB) thresholds for PROMIS physical function (PF) and pain interference (PI) in lumbar or thoracolumbar spine surgery population.

Summary of Background Data.
Patient-reported outcome measures (PROMs) are widely used in spine surgery to assess treatment efficacy. SCB is a relatively new concept that represents a substantial improvement perceived by the patient.

Methods.
This is a prospective study that included adults aged 21-85 years, undergoing lumbar/ thoracolumbar surgery for degenerative spine disease, and reporting at least 3/10 back or leg pain on a numeric rating scale. PROMs including Oswestry Disability Index, PROMIS PF, and PROMIS PI were collected preoperatively and at one year postoperatively. The North American Spine Surgery Patient Satisfaction (NASS) Index was collected one year postoperatively. SCB thresholds of absolute and percentage changes were calculated using anchor-based methods with ODI and NASS index as anchors. ROC analysis was used to determine optimal SCB cutoffs.

Results.
We included 137 patients. Using a fixed 19-point reduction in ODI as an anchor yielded SCB thresholds of 6.8 and 11.3 points for PROMIS PF and PI respectively. When using a dynamic anchor based on preoperative disability (50% ODI improvement), SCB thresholds were defined as achieving 18 and 27% of maximum possible improvement for PROMIS PF and PI respectively. Using NASS index, thresholds were 11 points or 24% for PROMIS PF, and 11.2 points or 21% for PROMIS PI. ROC values ranged from 0.81 to 0.9, with the dynamic ODI anchor cutoffs demonstrating the best discrimination.

Conclusion.
Our study is the first to define SCB thresholds for PROMIS PF and PROMIS PI using both fixed and dynamic cutoffs based on preoperative disability in lumbar and thoracolumbar patients. These thresholds will help in patient counseling and outcome evaluation for spine surgery research.
Real-world Plasma Exposure of Nirmatrelvir/Ritonavir in Chinese Hospitalized Patients With COVID-19: A Multicenter Retrospective Study
Authors: Ma Zhiyuan , Bai Mengru , Shen Shuying , Zhou Junshan , Dong Rong , Zhang Jiangjun , Weng Yayun , Li Li , Li Yongchen , Liu Dan , Yan Wei , Lin Nengming , Xia Jianmei 
Published: January 2025

Background:
Nirmatrelvir/ritonavir is licensed for the treatment of mild-to-moderate coronavirus disease (COVID-19) in patients at an increased risk of progression to severe disease. However, data on the real-world plasma exposure to nirmatrelvir/ritonavir remain limited, particularly in Chinese patients. This study aimed to assess the nirmatrelvir/ritonavir trough concentration (Ctrough) and identify its critical factors in hospitalized Chinese patients treated with nirmatrelvir/ritonavir 300 mg/100 mg twice daily over a 5-day course.

Methods:
A high-performance liquid chromatography-tandem mass spectrometry assay was developed and validated to measure the nirmatrelvir/ritonavir Ctrough. Correlation analyses were performed to identify the variables influencing nirmatrelvir/ritonavir Ctrough.

Results:
Among the 110 patients, 100% had plasma concentrations above the antiviral in vitro 90% effective concentration. The median Ctrough of nirmatrelvir was 4.55 mcg/mL (15.6× 90% effective concentration), ranging from 0.65 to 12.44 mcg/mL. Nirmatrelvir Ctrough in normal and mild renal impairment cohorts were comparable (4.09 ± 1.97 mcg/mL and 4.57 ± 2.21 mcg/mL) but significantly increased in the moderate renal impairment cohort (6.41 ± 2.31 mcg/mL). Sex, age, and obesity were not significantly associated with nirmatrelvir exposure.

Conclusions:
Nirmatrelvir Ctrough was high in Chinese patients with COVID-19, and therapeutic drug monitoring should not be routinely recommended, except in patients with renal impairment.
Cardiac sarcoidosis; update for the heart failure specialist
Authors: Birnie David H. 
Published: January 2025

Purpose of review
This review presents contemporary data on epidemiology, common presentations, investigations and diagnostic algorithms, treatment and prognosis. It particularly focuses on topics of most relevance to heart failure specialists, including what left ventricle (LV) function changes can be expected after treatment and outcomes to all standard and advanced heart failure therapies.

Recent findings
Around 5% of sarcoidosis patients have clinically manifest cardiac sarcoidosis (CS), presenting with significant arrhythmias (such as conduction disturbances and ventricular arrhythmias) or newly developed unexplained heart failure. These cardiac symptoms (including sudden cardiac death) may be the initial manifestations of CS. While cardiac magnetic resonance imaging (CMR) is the preferred method for identifying fibrosis in the myocardium, FDG-positron emission tomography (FDG-PET) helps in identifying active inflammation within the myocardium and aids in managing immunosuppressive treatment. The concept of isolated CS is much debated. However very importantly, recent data have shown that some patients diagnosed with ‘clinically and imaging isolated CS’ are subsequently found to have genetic cardiomyopathy. The management of CS involves a comprehensive approach including medications for immunosuppression, all standard heart failure medication and, in high-risk patient's implantable cardioverter defibrillators (ICDs). In CS patients with terminal heart failure who do not respond to medical and surgical interventions, heart transplantation and ventricular assist devices should be considered. Long-term results after transplantation are generally favorable and comparable to non-CS patients. The degree of left ventricular dysfunction remains a crucial prognostic factor in CS cases. Outcomes for CS have very significantly improved, over the last two decades due to earlier diagnosis, advanced heart failure treatments, and the strategic use of ICD therapy.

Summary
Outcomes for CS have significantly improved, over the last two decades due to earlier diagnosis, advanced heart failure treatments, and the strategic use of ICD therapy.
Multidimensional Classification and Prediction of Outcome Following Traumatic Brain Injury
Authors: Ponsford Jennie L. , Spitz Gershon , Pyman Phillipa , Carrier Sarah , Hicks Amelia J. , Nguyen Jack V. , Sander Angelle M. , Sherer Mark 
Published: January 2025

Objectives: This study aimed to identify outcome clusters among individuals with traumatic brain injury (TBI), 6 months to 10 years post-injury, in an Australian rehabilitation sample, and determine whether scores on 12 dimensions, combined with demographic and injury severity variables, could predict outcome cluster membership 1 to 3 years post-injury. Setting: Rehabilitation hospital. Participants: A total of 467 individuals with TBI, aged 17 to 87 (M = 44.2 years), 70% male, with mean post-traumatic amnesia 24 days (range 0.5-455 days), were assessed a mean of 3.4 years post-injury (range 0.5-10 years). A subgroup of 138 participants was also evaluated as rehabilitation inpatients and followed up 1 year post-injury. Design: Prospective observational study. Main Measures: TBI Quality of Life subscales (Upper Extremity, Pain Interference, Headache Pain, Anxiety, Resilience, Emotional and Behavioral Dyscontrol, General Cognitive Concerns, Independence, and Economic Quality of Life Scale), Neurobehavioral Symptom Inventory, Family Assessment Device General Functioning Scale, Wechsler Adult Intelligence Scale-IV Letter-Number-Sequencing and Coding, Rey Auditory Verbal Learning Test, Trail Making Test Part A, Verbal Fluency Test, Word Memory Test, Participation Assessment with Recombined Tools-Objective, and Glasgow Outcome Scale-Extended. Results: K-means cluster analysis revealed 5 clusters across 12 dimensions: Good Outcome, High Cognition, Poor Cognition, Poor Outcome, and Poor Adjustment, aligning with Sherer and colleagues’ clusters. Inpatient assessments (n = 138) identified profiles predictive of outcome group membership. Participants with Good Outcomes exhibited lower anxiety and higher independence, self-esteem, and resilience, despite some cognitive deficits. High Cognition correlated with robust Economic and Family Support. Poor Cognition aligned with impaired cognitive function but positive psychosocial ratings suggest limited self-awareness. Poor Outcome featured low initial cognitive scores and poor psychosocial adjustment. Poor Adjustment participants, without inpatient cognitive impairments, reported persistent pain, physical symptoms, and emotional distress. Conclusions: Findings support the evaluation of cognitive and psychosocial factors during rehabilitation to predict outcomes with potential to inform rehabilitative interventions to optimize outcomes.
Intermittent Fetal Heart Monitoring Through Moyo Doppler Improves Nonreassuring Fetal Heart Rate Detection in Hospital of Ethiopia
Authors: Fikadu Kassahun , Kote Mesfin , Hailemariam Zeleke , Shibru Tamiru , Koira Getahun , Chufamo Nega , Mulugeta Aregahegn , Belgu Belete , Mazengia Fikadu , Ayele Tadesse Awoke 
Published: January 2025

Purpose:
This study was aimed to assess the effect of intermittent fetal heart rate (FHR) monitoring using Moyo Doppler compared with fetoscope in hospitals of Ethiopia, 2023.

Background:
To facilitate more prompt identification of a hypoxic fetus, Laerdal Global Health has recently introduced the Moyo FHR monitor. Nevertheless, there exists limited knowledge regarding its efficacy derived from multicenter contextual trials conducted in resource-constrained environments, specifically in Ethiopia.

Methods:
This randomized trial (PACTR202305607000259) enrolled 2518 low-risk laboring women in the study during the study period, using a simple randomization technique from September 28, 2022, to February 28, 2023. A total of 1259 and 1259 were followed by Moyo and Pinard fetoscope, respectively. A P-value of less than .05 was considered significant.

Results:
The abnormal FHR was detected among 60 women (5.1%) and 30 women (2.4%) (P = .001) in the Moyo and Pinard fetoscope arms, respectively.

Conclusion:
The Moyo FHR monitor has demonstrated efficacy in detecting abnormal FHRs when compared with the Pinard fetoscope.

Implications for Practice and Research:
It is recommended that healthcare systems in low-resource settings consider implementing the Moyo device for FHR monitoring.
A model of care redesign within rheumatology: A mixed methods approach integrating nurse practitioners and physician assistants
Authors: Carnago Lisa , Holbrook Kristin , Leverenz David , Dimsdale Allison 
Published: January 2025

ABSTRACT

Background:
Increasing patient demand and clinician burnout in rheumatology practices have highlighted the need for more efficient models of care (MOC). Interprofessional collaboration is essential for improving patient outcomes and clinician satisfaction.

Local problem:
Our current MOC lacks standardization and formal integration of Nurse Practitioners (NPs) and Physician Assistants (PAs), resulting in reduced clinician satisfaction and limited patient access. To optimize care quality, clinician satisfaction, and patient access, we sought to develop an interprofessional MOC tailored to an academic rheumatology practice.

Methods:
We used a mixed methods sequential-exploratory design within a quality improvement (QI) framework to create a blueprint for MOC redesign.

Intervention:
Intervention development proceeded in four phases: needs assessment, data collection, socializing key ideas, and team design and planning.

Results:
In the needs assessment phase, divisional leadership was interviewed to identify shared goals for an optimized MOC. Data collection included surveys distributed to 12 physicians and 8 NPs/PAs, addressing 11 key domains related to current and future MOC needs. In phase 3, we communicated key findings to divisional leadership, clinicians, and staff. Phase 4 involved iterative team building and MOC design. Survey results revealed low satisfaction with the current MOC and a strong preference for parallel practice, standardization, and formal NP/Physician Assistant integration. Several barriers to MOC implementation were also identified.

Conclusion:
Redesigning the MOC in rheumatology requires aligning clinician, leadership, and organizational priorities. A mixed methods QI approach effectively uncovers clinical needs and potential barriers, supporting the successful implementation of a new MOC.
Metabolic dysfunction associated steatotic liver and kidney stones: what is going on?
Authors: Cunneely Owen P. , Roberts Anne , Fargue Sonia , Knight John , Assimos Dean G. , Wood Kyle D. 
Published: January 2025

Purpose of review
Metabolic dysfunction associated steatotic liver disease (MASLD) is increasing throughout the world, affecting nearly one in three individuals. Kidney stone disease, which is also increasing, is associated with MASLD. Common risk factors for both, including obesity, diabetes, dyslipidemia, hypertension, and metabolic syndrome, are likely drivers of this association. We present here a review of the associations and possible interconnections between these two common disease processes.

Recent findings
Epidemiological studies are discordant regarding the impact of sex on this association and on the impact of MASLD on incident stone risk. The nature of kidney stones is rarely taken into account.
A favorable milieu for uric acid kidney stone formation may be created by a lower urine pH resulting from defective ammonium production associated with insulin resistance, common in MASLD.
Endogenous oxalate synthesis, a major risk factor for calcium oxalate kidney stones, may be increased in MASLD via decline in the activity of enzymes involved in the detoxification of glyoxylate, the immediate precursor of oxalate.

Summary
The nature of kidney stones associated with MASLD and factors driving this association remain to be elucidated. Potential mechanisms identified underlying this include an increase in the risk factors for both uric acid and calcium oxalate kidney stones.