bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fuzzy kernel evidence Random Forest for identifying pseudouridine sites
Authors: Chen Mingshuai , Sun Mingai , Su Xi , Tiwari Prayag , Ding Yijie 
Published: April 2024

Abstract
Pseudouridine is an RNA modification that is widely distributed in both prokaryotes and eukaryotes, and plays a critical role in numerous biological activities. Despite its importance, the precise identification of pseudouridine sites through experimental approaches poses significant challenges, requiring substantial time and resources.Therefore, there is a growing need for computational techniques that can reliably and quickly identify pseudouridine sites from vast amounts of RNA sequencing data. In this study, we propose fuzzy kernel evidence Random Forest (FKeERF) to identify pseudouridine sites. This method is called PseU-FKeERF, which demonstrates high accuracy in identifying pseudouridine sites from RNA sequencing data. The PseU-FKeERF model selected four RNA feature coding schemes with relatively good performance for feature combination, and then input them into the newly proposed FKeERF method for category prediction. FKeERF not only uses fuzzy logic to expand the original feature space, but also combines kernel methods that are easy to interpret in general for category prediction. Both cross-validation tests and independent tests on benchmark datasets have shown that PseU-FKeERF has better predictive performance than several state-of-the-art methods. This new method not only improves the accuracy of pseudouridine site identification, but also provides a certain reference for disease control and related drug development in the future.
Neuroimaging and plasma evidence of early white matter loss in Parkinson’s disease with poor outcomes
Authors: Zarkali Angeliki , Hannaway Naomi , McColgan Peter , Heslegrave Amanda J , Veleva Elena , Laban Rhiannon , Zetterberg Henrik , Lees Andrew J , Fox Nick C , Weil Rimona S 
Published: April 2024

Abstract
Parkinson’s disease is a common and debilitating neurodegenerative disorder, with over half of patients progressing to postural instability, dementia or death within 10 years of diagnosis. However, the onset and rate of progression to poor outcomes is highly variable, underpinned by heterogeneity in underlying pathological processes. Quantitative and sensitive measures predicting poor outcomes will be critical for targeted treatment, but most studies to date have been limited to a single modality or assessed patients with established cognitive impairment. Here, we used multimodal neuroimaging and plasma measures in 98 patients with Parkinson’s disease and 28 age-matched controls followed up over 3 years. We examined: grey matter (cortical thickness and subcortical volume), white matter (fibre cross-section, a measure of macrostructure; and fibre density, a measure of microstructure) at whole-brain and tract level; structural and functional connectivity; and plasma levels of neurofilament light chain and phosphorylated tau 181. We evaluated relationships with subsequent poor outcomes, defined as development of mild cognitive impairment, dementia, frailty or death at any time during follow-up, in people with Parkinson’s disease. We show that extensive white matter macrostructural changes are already evident at baseline assessment in people with Parkinson’s disease who progress to poor outcomes (n = 31): with up to 19% reduction in fibre cross-section in multiple tracts, and a subnetwork of reduced structural connectivity strength, particularly involving connections between right frontoparietal and left frontal, right frontoparietal and left parietal and right temporo-occipital and left parietal modules. In contrast, grey matter volumes and functional connectivity were preserved in people with Parkinson’s disease with poor outcomes. Neurofilament light chain, but not phosphorylated tau 181 levels were increased in people with Parkinson’s disease with poor outcomes, and correlated with white matter loss. These findings suggest that imaging sensitive to white matter macrostructure and plasma neurofilament light chain may be useful early markers of poor outcomes in Parkinson’s disease. As new targeted treatments for neurodegenerative disease are emerging, these measures show important potential to aid patient selection for treatment and improve stratification for clinical trials.
Bipolar radiofrequency ablation for re-entrant ventricular tachycardia of right bundle branch block and left bundle branch block morphologies with the common slow conduction zone at the left ventricular summit: a case report
Authors: Toba Masahiro , Nasu Toshihiro , Nekomiya Nobuyoshi , Makino Takao , Yokoshiki Hisashi 
Published: April 2024

Abstract

Background
The left ventricular (LV) summit has anatomical limitations, so the detailed mapping is difficult. Therefore, the mechanism of ventricular tachycardia (VT) originating from the LV summit is not well understood.

Case summary
A 70-year-old man had VTs with right bundle branch block (VT1 and VT3) and left bundle branch block (VT2) morphologies originating from the left ventricular summit (LV summit). During the VT2 and VT3, fragmented potentials, which occurred earlier than the QRS onset, were recorded from bipolar electrodes of a catheter at the anterior intraventricular vein (AIV). By pacing from right ventricular apex, constant and progressive fusion were observed. During the entrainment pacing, the fragmented potentials in the AIV catheter were activated orthodromically and those in the His bundle were activated antidromically. In addition, there were two components of the ventricular electrogram at the LV summit area with the interval of more than 100 ms during the VTs. We performed bipolar radiofrequency ablation between the LV endocardium and AIV, and the VTs became non-inducible.

Discussion
Non-sustained VT/premature ventricular contraction originating from LV summit is generally considered to occur due to abnormal automaticity or triggered activity. In contrast, using entrainment technique, we demonstrated that the VTs with multiple morphologies were sustained with a re-entrant mechanism. Fragmentated potentials recorded in the AIV catheter were activated orthodromically with the entrainment pacing, indicating the slowly conducting isthmus. The intramural VT substrate was also suggested with a prolonged conduction time between the two ventricular components during the VTs.
Habitat and Respiratory Strategy Effects on Hypoxia Performance in Anuran Tadpoles
Authors: Phillips Jackson R , Nicolau Gary K , Ngwenya Shane S , Jackson Emily A , Womack Molly C 
Published: April 2024

Synopsis
A critical component of animal conservation in a changing world is an understanding of the physiological resilience of animals to different conditions. In many aquatic animals, hypoxia (low environmental oxygen levels) is a regular occurrence, but the likelihood and severity of hypoxia vary across habitats. Fast-flowing, stream-like habitats are never hypoxic, so long as flow is maintained. Do animals from such habitats retain the capacity to survive hypoxic conditions? We use aquatic frog tadpoles to test the effects of natural habitat on performance in hypoxia in an experimental framework, finding that stream-living tadpoles have reduced performance in hypoxia. Tadpoles also vary in lung presence, with some species able to breathe air during hypoxia. We found that among lunged tadpoles, air-breathing rates increase in hypoxia in pond-living species but not stream-living species. Lung presence was also found to influence hypoxia performance, as lungless, stream-living tadpoles were found to be especially vulnerable to hypoxia, while pond-living, lungless tadpoles appeared largely resilient to hypoxia. We consider the ramifications of our findings on conservation outlooks and strategies for frogs and their tadpoles, suggesting that stream-living tadpoles, and especially lungless, stream-living tadpoles, may be particularly at risk to factors that reduce stream flow. Thus, a primary goal for conservation and management of species with stream-living tadpoles should be the maintenance of year-round streamflow, which oxygenates waters and prevents hypoxia.
Eosinophil plasticity and diversity: proceedings of the 2023 International Eosinophil Society Symposium
Authors: Denburg Judah A , O’Byrne Paul M , Gauvreau Gail M 
Published: April 2024

Abstract
This issue highlights and details the program and scientific presentations at the International Eosinophil Society's 12th biennial symposium, which was held in Hamilton, Ontario, Canada, in July 2023. The meeting included sessions on regulation of eosinophil development; cell death, stress, and autophagy in eosinophils; local immunity interactions of eosinophils with multiple cell types; eosinophils in host defense; eosinophils and mast cells in gastrointestinal disorders; reciprocal interactions between eosinophils and the microbiome in homeostasis and dysbiosis; and eosinophils in tissue injury and repair and in tumor biology and cancer therapy. There was a mixture of special invited lectures and cutting-edge abstracts on specific aspects of eosinophil science, as well as enlivened pro-con debates on targeting eosinophils with biologics. A major thrust and overarching theme was that eosinophils exhibit remarkable plasticity and heterogeneity in executing their functions both in homeostasis and in pathobiology; there is a new “eo-verse” to understand. We trust that this special volume of the Journal of Leukocyte Biology will be of interest across many disciplines and medical subspecialties in biomedical sciences and demonstrate both the complexity and versatility of the eosinophil in biology and medicine.
Regulation of ICAM-1 in human neutrophils
Authors: Vignarajah Muralie , Wood Alexander J T , Nelmes Elizabeth , Subburayalu Julien , Herre Jurgen , Nourshargh Sussan , Summers Charlotte , Chilvers Edwin R , Farahi Neda 
Published: April 2024

Abstract
Intercellular cell adhesion molecule 1 (ICAM-1) is a cell surface glycoprotein with a vital role in the immune response to pathogens. The expression pattern of ICAM-1 is wide ranging, encompassing endothelial cells, epithelial cells, and neutrophils. Recent work has characterized the role of ICAM-1 in murine neutrophils, but the function of human neutrophil ICAM-1 is incompletely understood. Herein, we investigated the expression and role of ICAMs in human neutrophils in vitro and in vivo. Our findings show clear expression of ICAM-1, -3, and -4 on peripheral blood–derived neutrophils and demonstrate that the pathogen-associated molecular pattern lipoteichoic acid is an inducer of ICAM-1 expression in vitro. In vivo, neutrophils obtained from the pleural cavity of patients with a parapneumonic effusion display enhanced expression of ICAM-1 compared with peripheral blood– and oral cavity–derived neutrophils. Moreover, migration of peripheral blood–derived neutrophils across endothelial cells can upregulate neutrophil ICAM-1 expression. These findings indicate that pathogen-associated molecular patterns and/or cytokines, alongside transmigration, enhance neutrophil ICAM-1 expression at sites of inflammation. Mechanistically, we observed that ICAM-1high neutrophils display elevated S. aureus phagocytic capacity. However, unlike murine neutrophils, ICAM-1 intracellular signaling in human neutrophils was not essential for phagocytosis of Staphylococcus aureus and reactive oxygen species generation. Taken together, these results have important implications for the regulation of neutrophil-mediated pathogen clearance.
Comorbidity profiling identifies potential subtype of elderly patients with nasopharyngeal carcinoma
Authors: Li Ying , Pan Yuhui , Huang Zongwei , Wu Lishui , Wu Wenxi , Xu Siqi , Chen Zihan , Chen Xin , Lu Jun , Qiu Sufang 
Published: April 2024

Abstract

Background
Few studies have assessed the comprehensive associations among comorbid diseases in elderly patients with nasopharyngeal carcinoma (NPC). This study sought to identify potential comorbidity patterns and explore the relationship of comorbidity patterns with the mortality risk in elderly patients with NPC.

Methods
A total of 452 elderly patients with NPC were enrolled in the study. The network analysis and latent class analysis were applied to mine comorbidity patterns. Propensity score matching was used for adjusting confounders. A restricted cubic spline model was used to analyze the nonlinear association between age and the risk of all-cause mortality.

Results
We identified 2 comorbidity patterns, metabolic disease-related comorbidity (MDRC) and organ disease-related comorbidity (ODRC) in elderly patients with NPC. Patients in MDRC showed a significantly higher risk of all-cause mortality (71.41% vs 87.97%, HR 1.819 [95% CI, 1.106-2.994], P = .031) and locoregional relapse (68.73% vs 80.88%, HR 1.689 [95% CI, 1.055-2.704], P = .042). Moreover, in patients with MDRC pattern, we observed an intriguing inverted S-shaped relationship between age and all-cause mortality among patients aged 68 years and older. The risk of mortality up perpetually with age increasing in ODRC group, specifically within the age range of 68-77 years (HR 4.371, 1.958-9.757).

Conclusion
Our study shed light on the potential comorbidity patterns in elderly patients with NPC, thereby providing valuable insights into the development of comprehensive health management strategies for this specific population.
Preliminary Results of Calcaneal Lengthening Osteotomy Combined With Extra-articular Subtalar Arthrodesis for Severe Pes Planovalgus Deformity in Children With Cerebral Palsy
Authors: Bilgili Fuat , Demirel Mehmet , Koyuncu Dağhan 
Published: April 2024

Objective:
Pes planovalgus is the most common foot deformity seen in patients with cerebral palsy (CP). There are several different treatment modalities to treat this condition. Single or double calcaneal osteotomies, extra-articular arthrodesis, calcaneo-cuboido-cuneiform osteotomy, intraarticular arthrodesis, and arthroereisis are some of these modalities. Currently, there is insufficient information to determine the most effective treatment approach for pes planovalgus in children with CP. The aim of this study is to show the short to mid-term results of the new technique which combines calcaneus lengthening osteotomy, extra-articular subtalar arthrodesis, and soft tissue reconstruction that aims to decrease recurrence and complication rates of pes planovalgus surgery for patients with ambulatory CP.

Methods:
Patients with CP who were treated with calcaneal lengthening surgery and extra-articular subtalar arthrodesis between 2018 and 2021 were investigated retrospectively. All patients were ambulatory and Gross Motor Function Classification System I-II-III. Functional levels of the patients were assessed with the American Orthopaedic Foot and Ankle Society, Ankle-Hindfoot Score, and the Foot and Ankle Ability Score (Foot and Ankle Ability Measure) in preoperative and postoperative periods. On anteroposterior x-rays, talus-first metatarsal, talocalcaneal, talonavicular coverage angle and on lateral x-rays talus-first metatarsal, talocalcaneal, calcaneal inclination angle and talar tilt angle were evaluated.

Results:
The mean follow-up was 46 (range: 36 to 60) months. The mean American Orthopaedic Foot and Ankle Society increased from 41 (20 to 79) to 74 (38 to 93; P < 0.001). The mean Foot and Ankle Ability Measure increased significantly from 35 (7 to 73) to 54 (29 to 96; P<0.001). Clinical results were “satisfactory” for 32 feet, while they were “unsatisfactory” for 2 feet. Significant deformity correction was observed in all radiologic parameters.

Conclusion:
Our technique is found to be efficient for patients with Gross Motor Function Classification System I-II-III CP with pes planovalgus deformity. In short to mid-term follow-up, the technique achieved successful clinical and radiologic results with low complication rates. Superiority of this technique compared with the traditional ones can only be shown with randomized prospective studies.

Level of Evidence:
Level III—retrospective cohort study.
Patient-Reported Dry Eye Treatment and Burden of Care
Authors: Nau Cherie B. , Nau Amy C. , Fogt Jennifer S. , Harthan Jennifer S. , Shorter Ellen S. , Schornack Muriel M. 
Published: April 2024

Objectives:
Dry eye is a common condition that can decrease the quality of life. This survey-based study of persons with dry eye investigated self-reported treatments (initial, current), out-of-pocket expenses, time spent on self-management, sources of care, and sources of information about their condition.

Methods:
Online dry eye newsletters and support groups were emailed a link to an electronic survey asking members to participate. Survey respondents were not required to answer every question.

Results:
In total, 639 persons with self-reported dry eye responded (86% women, 14% men [n=623]; mean ± SD age, 55 ± 14 years [n=595]). Artificial tears were the most reported intervention (76% initially, 71% currently). The median (interquartile range) out-of-pocket treatment cost annually was $500 ($200–$1,320 [n=506]). In addition, 55% (n=544) estimated 5 to 20 min daily on self-management; 22% spent an hour or more. Ophthalmologists provided most dry eye care (67%, n=520). Only 48% (n=524) reported that their primary source of dry eye information came from their eye care clinician.

Conclusions:
Artificial tears are the primary treatment for dry eye. Ophthalmologists provide most dry eye care, but half of patients report that their eye care provider is not their primary source of information. Almost one fourth of patients spend an hour or more daily on treatments.
Long-term prognosis of patients with gallbladder carcinoma after curative-intent resection based on changes in the ratio of carbohydrate antigen 19-9 to total bilirubin (CA19-9/TB): a multicenter retrospective cohort study
Authors: Li Xue-Lei , Liu Zhi-Peng , Su Xing-Xing , Gong Yi , Yang Yi-Shi , Zhao Xiao-Lin , Li Zi-Mu , Ding Jun-Jie , Zhu Yi , Yin Da-Long , Yu Chao , Zhou Jin-Xue , Zhang Dong , Ding Rui , Chen Wei , Cheng Yao , Yue Ping , Wang Zi-Ran , Zhang Yan-Qi , Jiang Yan , Yin Xian-Yu , Bai Jie , Dai Hai-Su , Lau Wan Yee , Chen Zhi-Yu ,   The Biliary Surgery Branch of Elite Group of Chinese Digestive Surgery (EGCDS)
Published: April 2024

Background:
The prognostic value of carbohydrate antigen 19-9 (CA19-9) is known to be affected by elevated bilirubin levels in patients with gallbladder carcinoma (GBC). The clinical significance of changes in the ratio of CA19-9 levels to total bilirubin (TB) levels in patients with GBC after curative-intent resection remains unknown. The aim of this study was to determine the prognostic value of changes in preoperative and postoperative CA19-9/TB ratio in these patients.

Methods:
Prospectively collected data on consecutive patients who underwent curative-intent resection for GBC between January 2015 and December 2020 stored in a multicenter database from 10 hospitals were analyzed in this retrospective cohort study. Based on the adjusted CA19-9 defined as the ratio of CA19-9 to TB, and using 2×103 U/µmol as the upper normal value, patients were divided into a normal group (with normal preoperative and postoperative adjusted CA19-9), a normalization group (with abnormal preoperative but normal postoperative adjusted CA19-9), and a non-normalization group (with abnormal postoperative adjusted CA19-9). The primary outcomes were overall survival (OS) and recurrence-free survival (RFS). The log-rank test was used to compare OS and RFS among the groups. The Cox regression model was used to determine factors independently associated with OS and RFS.

Results:
The normal group (n=179 patients) and the normalization group (n=73 patients) had better OS and RFS than the non-normalization group (n=65 patients) (the 3-year OS rates 72.0%, 58.4% and 24.2%, respectively; the RFS rates 54.5%, 25.5% and 11.8%, respectively; both P<0.001). There were no significant differences between the normal and the normalization groups in OS and RFS (OS, P=0.255; RFS, P=0.130). Cox regression analysis confirmed that the non-normalization group was independently associated with worse OS and RFS. Subgroup analysis revealed that the non-normalization group of patients who received adjuvant therapy had significantly improved OS and RFS as compared to those who did not receive adjuvant therapy (OS, P=0.025; RFS, P=0.003).

Conclusions:
Patients with GBC who underwent curative-intent surgical resection with postoperative abnormal levels of adjusted CA19-9 (the CA19-9/TB ratio) were associated with poorer long-term survival outcomes. Adjuvant therapy after surgery improved the long-term outcomes of these patients.
Pituitary stalk interruption syndrome: a case report and literature review
Authors: Ali Alqarni Abdullah , Abdalla Khalid Mohamed , Alqarni Mohammed A. S. , Alfaifi Jaber A. , Osman Hisham G. A. , Al Alhindi Bandar S. 
Published: April 2024

Background:
Pituitary stalk interruption syndrome is a rare congenital anomaly of the pituitary gland characterized by growth hormones deficiency (with or without other pituitary hormone deficiencies) along with radiological features of a thin or interrupted pituitary stalk, an ectopic or absent posterior pituitary, or a hypoplastic or absent anterior pituitary.

Case presentation:
A 10-year-old baby boy came with short stature. The laboratory investigations were done and showed low growth hormones and low thyroid-stimulating hormone. MRI showed an ectopic posterior pituitary, a small hypoplastic anterior pituitary, and an absent pituitary stalk.

Conclusion:
Pituitary stalk interruption syndrome is a very rare entity. MRI is used to diagnose it. Early detection of this syndrome improve the patient symptoms especially before puberty.
No Improvement in Intention-to-treat Survival and Increasing Liver Nonutilization Rate During the MELD Era
Authors: Matsumoto Rei , Verna Elizabeth C. , Rosenblatt Russell , Emond Jean C. , Brown Robert S. , Rahnemai-Azar Amir A. , Samstein Benjamin , Dove Lorna M. , Kato Tomoaki 
Published: April 2024

Background.
Although post liver transplant survival rates have significantly improved during the past 2–3 decades, the trend in intention-to-treat (ITT) survival (survival from waitlist addition) has not been well studied.

Methods.
We conducted a retrospective analysis of Scientific Registry of Transplant Recipients data to determine the trend in ITT survival in liver transplant candidates. Adult (age ≧ 18 y) patients who were on the waitlist between the time period of March 1, 2002, to December 31, 2019 (n = 200 816) and deceased liver donors that were registered between the same time period (n = 152 593) were analyzed.

Results.
We found a constant increase in posttransplant survival rates; however, the ITT survival rates showed no statistically significant improvement through the study period. We observed significant linear increase in waitlist dropout rates over time. We also observed linear increase in liver nonutilization rate in both entire cases and brain-dead cases. Donor risk index increased significantly over the years; however, it was mostly driven by increase in donation after circulatory death cases; without donation after circulatory death cases, donor risk index was stable throughout the 17 y we observed.

Conclusions.
The reason of the increased liver nonutilization rate is unclear; however, it is possible that reluctance to use high-risk organ to maintain better posttransplant outcomes contributed to this increase, which also could have led to increase in waitlist dropout rates and no improvements in ITT survival. Further investigation is warranted on the increased nonutilization rates to improve over all contribution of liver transplant to patient care.