bluuebunny/crossref_metadata_2025_split huggingface dataset:
RNA modulates hnRNPA1A amyloid formation mediated by biomolecular condensates
Authors: Morelli Chiara , Faltova Lenka , Capasso Palmiero Umberto , Makasewicz Katarzyna , Papp Marcell , Jacquat Raphaël P. B. , Pinotsi Dorothea , Arosio Paolo 
Published: March 2024

AbstractSeveral RNA binding proteins involved in membraneless organelles can form pathological amyloids associated with neurodegenerative diseases, but the mechanisms of how this aggregation is modulated remain elusive. Here we investigate how heterotypic protein–RNA interactions modulate the condensation and the liquid to amyloid transition of hnRNPA1A, a protein involved in amyothropic lateral sclerosis. In the absence of RNA, formation of condensates promotes hnRNPA1A aggregation and fibrils are localized at the interface of the condensates. Addition of RNA modulates the soluble to amyloid transition of hnRNPA1A according to different pathways depending on RNA/protein stoichiometry. At low RNA concentrations, RNA promotes both condensation and amyloid formation, and the catalytic effect of RNA adds to the role of the interface between the dense and dilute phases. At higher RNA concentrations, condensation is suppressed according to re-entrant phase behaviour but formation of hnRNPA1A amyloids is observed over longer incubation times. Our findings show how heterotypic nucleic acid–protein interactions affect the kinetics and molecular pathways of amyloid formation.
Remnants of shifting early Cenozoic Pacific lower mantle flow imaged beneath the Philippine Sea Plate
Authors: Fan Jianke , Zhao Dapeng , Li Cuilin , Liu Lijun , Dong Dongdong 
Published: March 2024

AbstractSeismic anisotropy could provide vital information about the evolution and internal convection of the deep Earth interior. Although previous seismological studies have revealed a wide distribution of seismic anisotropy in the upper portion of the lower mantle beneath many subduction zones, the existence of anisotropy at these depths away from subducted slabs remains debated. Here we use P-wave azimuthal anisotropy tomography to image the crust and mantle down to 1,600-km depth. We find prominent anisotropic patterns in the upper portion of the lower mantle beneath the Philippine Sea Plate. Substantial azimuthal anisotropy with N–S fast-velocity directions occurs at 700–900-km depths. We interpret this azimuthal anisotropy as a remnant of the Pacific lower mantle flow field about 50 million years ago. Two isolated high-velocity anomalies at 700–1,600-km depths may be vestigial pieces of the subducted Izanagi slab with seismic velocity features suggesting a shift in the Pacific lower mantle flow field by about 40 million years ago. Our findings provide seismic evidence for the existence of complex lower mantle flows and deformation mechanisms away from subduction zones.
Classification and automatic scoring of arousal intensity during sleep stages using machine learning
Authors: Han Hyewon , Seong Min Jae , Hyeon Janghun , Joo Eunyeon , Oh Junhyoung 
Published: March 2024

AbstractArousal during sleep can result in sleep fragmentation and various physiological effects, impairing cognitive function and raising blood pressure and heart rate. However, the current definition of arousal has limitations in assessing both amplitude and duration, making it challenging to measure sleep fragmentation accurately. Moreover, there is inconsistency among inter-raters in arousal scoring, which renders it susceptible to subjective variability. Therefore, this study aims to identify a highly accurate classifier for each sleep stage by employing optimized feature selection and machine learning models. According to electroencephalography (EEG) signals during the arousal phase, the intensity level was categorized into four levels. For control, the non-arousal cases were used as level 0 and referred as sham arousal, resulting in five arousal intensity levels. Wavelet transform was applied to analyze sleep arousal to extract features from EEG. Based on these features, we classified arousal intensity levels through machine learning algorithms. Due to the different characteristics of EEG in each sleep stage, the classification model was optimized for the four sleep stages. Excluding sham arousals, a total of 13,532 arousal events were used. The lowest intensity in the entire data, level 1, was computed to be 3107, level 2 was 3384, level 3 was 3472, and the highest intensity of level 4 was 3,569. The optimized classification model for each sleep stage achieved an average sensitivity of 82.68%, specificity of 95.68%, and AUROC of 96.30%. The sensitivity of the control, arousal intensity level 0, was 83.07%, a 1.25% increase over the unoptimized model and a 14.22% increase over previous research. This study used machine learning techniques to develop classifiers for each sleep stage, improving the accuracy of arousal intensity classification. The classifiers showed high sensitivity and specificity and revealed the unique characteristics of arousal intensity during different sleep stages. These findings represent a novel approach to arousal research and have implications for developing more accurate predictive models in sleep research.
Compliance with Australian Orthopaedic Association guidelines does not reduce the risk of venous thromboembolism after total hip and knee arthroplasty
Authors: Badge Helen , Churches Tim , Naylor Justine M. , Xuan Wei , Armstrong Elizabeth , Gray Leeanne , Fletcher John , Gosbell Iain , Lin Chung-Wei Christine , Harris Ian A. 
Published: March 2024

AbstractPreventing avoidable venous-thrombo-embolism (VTE) is a priority to improve patient and service outcomes after total hip and total knee arthroplasty (THA, TKA), but compliance with relevant clinical guidelines varies. This study aims to determine the degree to which prophylaxis was compliant with Australian Orthopaedic Association (AOA) VTE prophylaxis guidelines and whether non-compliance is associated with increased risk of VTE. A prospective multi-centre cohort study of adults with osteoarthritis undergoing primary TKA/THA was completed at 19 high-volume public and private hospitals. Data were collected prior to surgery and for one-year post-surgery. Logistic regression was undertaken to explore associations between non-compliance with AOA VTE prophylaxis guidelines and symptomatic 90-day VTE outcomes. Data were analysed for 1838 participants from 19 sites. The rate of non-compliance with all clinical guideline recommendations was 20.1% (N = 369), with 14.1% (N = 259) non-compliance for risk-stratified prophylaxis, 35.8% (N = 658) for duration, and 67.8% (N = 1246) for other general recommendations. Symptomatic VTE was experienced up to 90-days post-surgery by 48 people (2.6%). Overall guideline non-compliance (AOR = 0.93, 95%CI = 0.4 to 1.3, p = 0.86) was not associated with a lower risk of symptomatic 90-day VTE. Results were consistent when people with high bleeding risk were excluded (AOR = 0.94, 95%CI = 0.44 to 2.34, p = 0.89). Non-compliance with the AOA VTE prophylaxis guidelines was not associated with risk of 90-day VTE after arthroplasty. This counterintuitive finding is concerning and necessitates a rigorous review of the AOA VTE prevention clinical guideline.
Hybrid similarity relation based mutual information for feature selection in intuitionistic fuzzy rough framework and its applications
Authors: Tiwari Anoop Kumar , Saini Rajat , Nath Abhigyan , Singh Phool , Shah Mohd Asif 
Published: March 2024

AbstractFuzzy rough entropy established in the notion of fuzzy rough set theory, which has been effectively and efficiently applied for feature selection to handle the uncertainty in real-valued datasets. Further, Fuzzy rough mutual information has been presented by integrating information entropy with fuzzy rough set to measure the importance of features. However, none of the methods till date can handle noise, uncertainty and vagueness simultaneously due to both judgement and identification, which lead to degrade the overall performances of the learning algorithms with the increment in the number of mixed valued conditional features. In the current study, these issues are tackled by presenting a novel intuitionistic fuzzy (IF) assisted mutual information concept along with IF granular structure. Initially, a hybrid IF similarity relation is introduced. Based on this relation, an IF granular structure is introduced. Then, IF rough conditional and joint entropies are established. Further, mutual information based on these concepts are discussed. Next, mathematical theorems are proved to demonstrate the validity of the given notions. Thereafter, significance of the features subset is computed by using this mutual information, and corresponding feature selection is suggested to delete the irrelevant and redundant features. The current approach effectively handles noise and subsequent uncertainty in both nominal and mixed data (including both nominal and category variables). Moreover, comprehensive experimental performances are evaluated on real-valued benchmark datasets to demonstrate the practical validation and effectiveness of the addressed technique. Finally, an application of the proposed method is exhibited to improve the prediction of phospholipidosis positive molecules. RF(h2o) produces the most effective results till date based on our proposed methodology with sensitivity, accuracy, specificity, MCC, and AUC of 86.7%, 90.1%, 93.0% , 0.808, and 0.922 respectively.
Predictors of the unfavorable outcomes in acute ischemic stroke patients treated with alteplase, a multi-center randomized trial
Authors: Zeinhom Mohamed G. , Khalil Mohamed Fouad Elsayed , Kamel Islam Fathallah Mohamed , Kohail Ahmed Mohamed , Ahmed Sherihan Rezk , Elbassiouny Ahmed , Shuaib Ashfaq , Al-Nozha Omar M 
Published: March 2024

AbstractWorldwide, stroke is a leading cause of long-term disability in adults. Alteplase is the only approved treatment for acute ischemic stroke (AIS) and results in an improvement in a third of treated patients. We evaluated the post-stroke unfavourable outcome predictors in alteplase-treated patients from Egypt and Saudi Arabia. We assessed the effect of different risk factors on AIS outcomes after alteplase in Egypt and Saudi Arabia. Our study included 592 AIS alteplase-treated patients. The relationship between risk factors, clinical presentation, and imaging features was evaluated to predict factors associated with poor outcomes. An mRS score of three or more was used to define poor outcomes. Poor outcome was seen in 136 patients (23%), and Patients with unfavourable effects had significantly higher admission hyperglycaemia, a higher percentage of diabetes mellitus, cardioembolic stroke, and a lower percentage of small vessel stroke. Patients with higher baseline NIHSS score (OR 1.39; 95% CI 1.12–1.71; P = 0.003), admission hyperglycaemia (OR 13.12; 95% CI 3.37–51.1; P < 0.001), and post-alteplase intracerebral haemorrhage (OR 7.41; 95% CI 1.69–32.43; P = 0.008) independently predicted unfavourable outcomes at three months. In AIS patients treated with alteplase, similar to reports from other regions, in patients from Egypt and Saudi Arabia also reveal that higher NIHSS, higher serum blood sugar, and post-alteplase intracerebral haemorrhage were the predictors of unfavourable outcomes three months after ischemic stroke.Trial registration: (clinicaltrials.gov NCT06058884), retrospectively registered on 28/09/2023.
Dual-energy computed tomography and micro-computed tomography for assessing bone regeneration in a rabbit tibia model
Authors: Su Danyang , Wu Yan , Yang Shenyu , Ma Duoshan , Zhang Haoran , Ma Yuanbo , Liu Jinlong , Wang Chunyu , Liu Huilong , Yang Xiaopeng 
Published: March 2024

AbstractTo gain a more meaningful understanding of bone regeneration, it is essential to select an appropriate assessment method. Micro-computed tomography (Micro-CT) is widely used for bone regeneration because it provides a substantially higher spatial resolution. Dual-energy computed tomography (DECT) ensure shorter scan time and lower radiation doses during quantitative evaluation. Therefore, in this study, DECT and Micro-CT were used to evaluate bone regeneration. We created 18 defects in the tibial plateau of the rabbits and filled them with porous polyetheretherketone implants to promote bone regeneration. At 4, 8, and 12 weeks, Micro-CT and DECT were used to assess the bone repair in the defect region. In comparison to Micro-CT (152 ± 54 mg/cm3), the calcium density values and hydroxyapatite density values obtained by DECT [DECT(Ca) and DECT(HAP)] consistently achieved lower values (59 ± 25 mg/cm3, 126 ± 53 mg/cm3). In addition, there was a good association between DECT and Micro-CT (R = 0.98; R2 = 0.96; DECT(Ca): y = 0.45x–8.31; DECT(HAP): y = 0.95x–17.60). This study highlights the need to use two different imaging methods, each with its advantages and disadvantages, to better understand the bone regeneration process.
Investigating the prevalence of body dysmorphic disorder among Jordanian adults with dermatologic and cosmetic concerns: a case–control study
Authors: Murshidi Rand , Hammouri Muhammad , Al-Ani Abdallah , Kitaneh Razi , Al-Soleiti Majd , Al Ta’ani Zain , Sweis Sami , Halasa Zeina , Fashho Eva , Arafah Malak , Almaani Noor , Abdallat Mahmoud , Al-Dar’awi Faten , Kittaneh Eman , Jaber Besan , Almudallal Farah , Smadi Zina 
Published: March 2024

AbstractBody Dysmorphic Disorder (BDD) is an underexplored psychiatric condition in Middle Eastern countries, particularly in patients with dermatologic concerns, where alterations in appearance may elevate the risk of BDD. We studied patients at Jordan University Hospital's general dermatology and cosmetic clinics from July to September 2022, comparing them to healthy controls. Patients with dermatologic conditions were evaluated per the International Classification of Diseases (ICD-10) criteria by trained dermatologists. All participants completed the Dysmorphic Concerns Questionnaire (DCQ), Perceived Stress Scale, Patient Health Questionnaire-2, General Anxiety Disorder Assessment tool-2. We assessed BDD prevalence using four DCQ cutoffs: 9, 11, 14, and 17, reporting effect sizes as odds ratios (OR). Our study involved 1500 participants, with an average age of 29.3 (± 14.8) years and a female-to-male ratio of 3.15-to-1. At the 9, 11, 14, and 17 DCQ cutoffs, BDD prevalence was 78.2%, 54.2%, 26.5%, and 11.7%, respectively. Patients with dermatologic concerns were more likely to exhibit clinical BDD symptoms than controls at the 11-cutoff (OR: 1.26; 95% CI 1.01–1.58; p < 0.05). Conversely, those with cosmetic concerns were more prone to clinical BDD than controls at cutoffs 9 (OR: 2.26; 95% CI 1.28–3.97; p < 0.05) and 11 (OR: 1.50; 95% CI 1.03–2.20; p < 0.05). Our logistic regression revealed consistent associations between higher DCQ scores and elevated anxiety, depression, perceived skin disease-related stigma, and reduced quality of life (p < 0.05). In conclusion, patients with dermatologic issues and those seeking cosmetic procedures are at significant risk of developing BDD, necessitating proactive screening and referrals for specialized care by dermatologists due to the associated psychological distress and unproductive consultations. Providing specialized training for healthcare professionals to establish an integrated care approach to address the needs of patients with BDD should be the focus of future research projects.
Effect of biological sewage sludge and its derived biochar on accumulation of potentially toxic elements by corn (Zea mays L.)
Authors: Namdari Maryam , Soleimani Mohsen , Mirghaffari Nourollah , Kharrazi Seyyedeh Maryam 
Published: March 2024

AbstractThe land application of sewage sludge can cause different environmental problems due to the high content of potentially toxic elements (PTEs). The objective of this study was to compare the effect of urban biological sewage sludge (i.e. the waste of activated sludge process) and its derived biochar as the soil amendments on the bioavailability of PTEs and their bioaccumulation by corn (Zea maysL.) under two months of greenhouse conditions. The soil was treated by adding biochar samples at 0 (control), 1, 3, 5% w/w. The diethylenetriamine pentaacetic acid (DTPA)-extractable concentrations of PTEs including Zn, Pb, Cd, Cr, Ni, Fe, and Cu in soil and their accumulation by plant shoot and root were measured. Conversion of the biological sewage sludge into the biochar led to decrease the PTEs bioavailability and consequently decreased their contents in plant tissues. The DTPA extractable metal concentrations of produced biochar in comparison to the biological sewage sludge reduced 75% (Cd), 65% (Cr), 79% (Ni and Pb), 76% (Zn), 91% (Cu) and 88% (Fe). Therefore, the content of Ni, Fe, Zn and Cd in corn shoot was decreased 61, 32, 18 and 17% respectively in application of 5% biochar than of raw sewage sludge. Furthermore, the application of 5% biochar enhanced the physiological parameters of the plants including shoot dry weight (twice) and wet weight (2.25 times), stem diameter (1.70 times), chlorophyll content (1.03 times) in comparison to using 5% raw sewage sludge. The results of the study highlight that application of the biochar derived from urban biological sewage sludge in soil could decrease the risk of PTEs to the plant.
Decoding gene regulatory circuitry underlying TNBC chemoresistance reveals biomarkers for therapy response and therapeutic targets
Authors: Lusby Ryan , Zhang Ziyi , Mahesh Arun , Tiwari Vijay K. 
Published: March 2024

AbstractTriple-negative breast cancer (TNBC) is the most aggressive breast cancer subtype characterised by extensive intratumoral heterogeneity, high rates of metastasis and chemoresistance, leading to poor clinical outcomes. Despite progress, the mechanistic basis of chemotherapy resistance in TNBC patients remains poorly understood. Here, leveraging single-cell transcriptome datasets of matched longitudinal TNBC chemoresponsive and chemoresistant patient cohorts, we unravel distinct cell subpopulations intricately associated with chemoresistance and the signature genes defining these populations. Notably, using genome-wide mapping of the H3K27ac mark, we show that the expression of these chemoresistance genes is driven via a set of TNBC super-enhancers and associated transcription factor networks across TNBC subtypes. Furthermore, genetic screens reveal that a subset of these transcription factors is essential for the survival of TNBC cells, and their loss increases sensitivity to chemotherapeutic agents. Overall, our study has revealed epigenetic and transcription factor networks underlying chemoresistance and suggests novel avenues to stratify and improve the treatment of patients with a high risk of developing resistance.
Predicting droplet detachment force: Young-Dupré Model Fails, Young-Laplace Model Prevails
Authors: Sadullah Muhammad Subkhi , Xu Yinfeng , Arunachalam Sankara , Mishra Himanshu 
Published: March 2024

AbstractLiquid droplets hanging from solid surfaces are commonplace, but their physics is complex. Examples include dew or raindrops hanging onto wires or droplets accumulating onto a cover placed over warm food or windshields. In these scenarios, determining the force of detachment is crucial to rationally design technologies. Despite much research, a quantitative theoretical framework for detachment force remains elusive. In response, we interrogated the elemental droplet–surface system via comprehensive laboratory and computational experiments. The results reveal that the Young–Laplace equation can be utilized to accurately predict the droplet detachment force. When challenged against experiments with liquids of varying properties and droplet sizes, detaching from smooth and microtextured surfaces of wetting and non-wetting chemical make-ups, the predictions were in an excellent quantitative agreement. This study advances the current understanding of droplet physics and will contribute to the rational development of technologies.
Variational Monte Carlo with large patched transformers
Authors: Sprague Kyle , Czischek Stefanie 
Published: March 2024

AbstractLarge language models, like transformers, have recently demonstrated immense powers in text and image generation. This success is driven by the ability to capture long-range correlations between elements in a sequence. The same feature makes the transformer a powerful wavefunction ansatz that addresses the challenge of describing correlations in simulations of qubit systems. Here we consider two-dimensional Rydberg atom arrays to demonstrate that transformers reach higher accuracies than conventional recurrent neural networks for variational ground state searches. We further introduce large, patched transformer models, which consider a sequence of large atom patches, and show that this architecture significantly accelerates the simulations. The proposed architectures reconstruct ground states with accuracies beyond state-of-the-art quantum Monte Carlo methods, allowing for the study of large Rydberg systems in different phases of matter and at phase transitions. Our high-accuracy ground state representations at reasonable computational costs promise new insights into general large-scale quantum many-body systems.
ATR limits Rad18-mediated PCNA monoubiquitination to preserve replication fork and telomerase-independent telomere stability
Authors: Chen Siyuan , Pan Chen , Huang Jun , Liu Ting 
Published: March 2024

AbstractUpon replication fork stalling, the RPA-coated single-stranded DNA (ssDNA) formed behind the fork activates the ataxia telangiectasia-mutated and Rad3-related (ATR) kinase, concomitantly initiating Rad18-dependent monoubiquitination of PCNA. However, whether crosstalk exists between these two events and the underlying physiological implications of this interplay remain elusive. In this study, we demonstrate that during replication stress, ATR phosphorylates human Rad18 at Ser403, an adjacent residue to a previously unidentified PIP motif (PCNA-interacting peptide) within Rad18. This phosphorylation event disrupts the interaction between Rad18 and PCNA, thereby restricting the extent of Rad18-mediated PCNA monoubiquitination. Consequently, excessive accumulation of the tumor suppressor protein SLX4, now characterized as a novel reader of ubiquitinated PCNA, at stalled forks is prevented, contributing to the prevention of stalled fork collapse. We further establish that ATR preserves telomere stability in alternative lengthening of telomere (ALT) cells by restricting Rad18-mediated PCNA monoubiquitination and excessive SLX4 accumulation at telomeres. These findings shed light on the complex interplay between ATR activation, Rad18-dependent PCNA monoubiquitination, and SLX4-associated stalled fork processing, emphasizing the critical role of ATR in preserving replication fork stability and facilitating telomerase-independent telomere maintenance.
The TAM, a Translocation and Assembly Module for protein assembly and potential conduit for phospholipid transfer
Authors: Goh Kwok Jian , Stubenrauch Christopher J , Lithgow Trevor 
Published: March 2024

AbstractThe assembly of β-barrel proteins into the bacterial outer membrane is an essential process enabling the colonization of new environmental niches. The TAM was discovered as a module of the β-barrel protein assembly machinery; it is a heterodimeric complex composed of an outer membrane protein (TamA) bound to an inner membrane protein (TamB). The TAM spans the periplasm, providing a scaffold through the peptidoglycan layer and catalyzing the translocation and assembly of β-barrel proteins into the outer membrane. Recently, studies on another membrane protein (YhdP) have suggested that TamB might play a role in phospholipid transport to the outer membrane. Here we review and re-evaluate the literature covering the experimental studies on the TAM over the past decade, to reconcile what appear to be conflicting claims on the function of the TAM.