bluuebunny/crossref_metadata_2025_split huggingface dataset:
Chemical versus physical pressure effects on the structure transition of bilayer nickelates
Authors: Wang Gang , Wang Ningning , Lu Tenglong , Calder Stuart , Yan Jiaqiang , Shi Lifen , Hou Jun , Ma Liang , Zhang Lili , Sun Jianping , Wang Bosen , Meng Sheng , Liu Miao , Cheng Jinguang 
Published: January 2025

AbstractThe observation of high-Tc superconductivity (HTSC) in concomitant with pressure-induced orthorhombic-tetragonal structural transition in bilayer La3Ni2O7 has sparked hopes of achieving HTSC by stabilizing the tetragonal phase at ambient pressure. Chemical pressure, introduced by replacing La3+ with smaller rare-earth R3+ has been considered as a potential route. However, our experimental and theoretical investigation reveals that such substitutions, despite causing lattice contraction, actually produce stronger orthorhombic distortions, requiring higher pressures for the structural transition. A linear extrapolation of Pc versus the average size of A-site cations (<rA>), yields a putative critical value of <rA>c ≈ 1.23 Å for Pc ≈ 1 bar. The negative correlation between Pc and <rA> indicates that replacing La3+ with smaller R3+ ions is unlikely to reduce Pc to ambient pressure. Instead, substituting La3+ with larger cations like Sr2+ or Ba2+ might be a feasible approach. Our results provide guidance for realizing ambient-pressure HTSC in bilayer nickelates.
Efficient micromirror confinement of sub-teraelectronvolt cosmic rays in galaxy clusters
Authors: Reichherzer Patrick , Bott Archie F. A. , Ewart Robert J. , Gregori Gianluca , Kempski Philipp , Kunz Matthew W. , Schekochihin Alexander A. 
Published: January 2025

AbstractCosmic rays (CRs) play a pivotal role in shaping the thermal and dynamical properties of astrophysical environments, such as galaxies and galaxy clusters. Recent observations suggest a stronger confinement of CRs in certain astrophysical systems than predicted by current CR-transport theories. Here, we show that the incorporation of microscale physics into CR-transport models can account for this enhanced CR confinement. We develop a theoretical description of the effect of magnetic microscale fluctuations originating from the mirror instability on macroscopic CR diffusion. We confirm our theory with large-dynamical-range simulations of CR transport in the intracluster medium (ICM) of galaxy clusters and kinetic simulations of CR transport in micromirror fields. We conclude that sub-teraelectronvolt CR confinement in the ICM is far more effective than previously anticipated on the basis of Galactic-transport extrapolations. The transformative impact of micromirrors on CR diffusion provides insights into how microphysics can reciprocally affect macroscopic dynamics and observable structures across a range of astrophysical scales.
Analysis of multi-condition single-cell data with latent embedding multivariate regression
Authors: Ahlmann-Eltze Constantin , Huber Wolfgang 
Published: January 2025

Abstract
Identifying gene expression differences in heterogeneous tissues across conditions is a fundamental biological task, enabled by multi-condition single-cell RNA sequencing (RNA-seq). Current data analysis approaches divide the constituent cells into clusters meant to represent cell types, but such discrete categorization tends to be an unsatisfactory model of the underlying biology. Here, we introduce latent embedding multivariate regression (LEMUR), a model that operates without, or before, commitment to discrete categorization. LEMUR (1) integrates data from different conditions, (2) predicts each cell’s gene expression changes as a function of the conditions and its position in latent space and (3) for each gene, identifies a compact neighborhood of cells with consistent differential expression. We apply LEMUR to cancer, zebrafish development and spatial gradients in Alzheimer’s disease, demonstrating its broad applicability.
Evaluating generalizability of oncology trial results to real-world patients using machine learning-based trial emulations
Authors: Orcutt Xavier , Chen Kan , Mamtani Ronac , Long Qi , Parikh Ravi B. 
Published: January 2025

Abstract
Randomized controlled trials (RCTs) evaluating anti-cancer agents often lack generalizability to real-world oncology patients. Although restrictive eligibility criteria contribute to this issue, the role of selection bias related to prognostic risk remains unclear. In this study, we developed TrialTranslator, a framework designed to systematically evaluate the generalizability of RCTs for oncology therapies. Using a nationwide database of electronic health records from Flatiron Health, this framework emulates RCTs across three prognostic phenotypes identified through machine learning models. We applied this approach to 11 landmark RCTs that investigated anti-cancer regimens considered standard of care for the four most prevalent advanced solid malignancies. Our analyses reveal that patients in low-risk and medium-risk phenotypes exhibit survival times and treatment-associated survival benefits similar to those observed in RCTs. In contrast, high-risk phenotypes show significantly lower survival times and treatment-associated survival benefits compared to RCTs. Our results were corroborated by a comprehensive robustness assessment, including examinations of specific patient subgroups, holdout validation and semi-synthetic data simulation. These findings suggest that the prognostic heterogeneity among real-world oncology patients plays a substantial role in the limited generalizability of RCT results. Machine learning frameworks may facilitate individual patient-level decision support and estimation of real-world treatment benefits to guide trial design.
Orthology inference at scale with FastOMA
Authors: Majidian Sina , Nevers Yannis , Yazdizadeh Kharrazi Ali , Warwick Vesztrocy Alex , Pascarelli Stefano , Moi David , Glover Natasha , Altenhoff Adrian M. , Dessimoz Christophe 
Published: January 2025

Abstract
The surge in genome data, with ongoing efforts aiming to sequence 1.5 M eukaryotes in a decade, could revolutionize genomics, revealing the origins, evolution and genetic innovations of biological processes. Yet, traditional genomics methods scale poorly with such large datasets. Here, addressing this, ‘FastOMA’ provides linear scalability for orthology inference, enabling the processing of thousands of eukaryotic genomes within a day. FastOMA maintains the high accuracy and resolution of the well-established Orthologous Matrix (OMA) approach in benchmarks. FastOMA is available via GitHub at https://github.com/DessimozLab/FastOMA/.
A membrane permeability database for nonpeptidic macrocycles
Authors: Feng Qiushi , De Chavez Danjo , Kihlberg Jan , Poongavanam Vasanthanathan 
Published: January 2025

AbstractThe process of developing new drugs is arduous and costly, particularly for targets classified as “difficult-to-drug.” Macrocycles show a particular ability to modulate difficult-to-drug targets, including protein-protein interactions, while still allowing oral administration. However, the determination of membrane permeability, critical for reaching intracellular targets and for oral bioavailability, is laborious and expensive. In silico methods are a cost-effective alternative, enabling predictions prior to compound synthesis. Here, we present a comprehensive online database (https://swemacrocycledb.com/), housing 5638 membrane permeability datapoints for 4216 nonpeptidic macrocycles, curated from the literature, patents, and bioactivity repositories. In addition, we present a new descriptor, the “amide ratio” (AR), that quantifies the peptidic nature of macrocyclic compounds, enabling the classification of peptidic, semipeptidic, and nonpeptidic macrocycles. Overall, this resource fills a gap among existing databases, offering valuable insights into the membrane permeability of nonpeptidic and semipeptidic macrocycles, and facilitating predictions for drug discovery projects.
One-week test-retest recordings of resting cardiorespiratory data for reliability analysis
Authors: Schumann Andy , Lukas Franziska , Rieger Katrin , Gupta Yubraj , Bär Karl-Jürgen 
Published: January 2025

AbstractHeart rate variability (HRV) is a key indicator of cardiac autonomic function, making reliable assessment crucial. To examine the test-retest stability of resting HRV in healthy individuals, fifty participants attended two lab sessions within a week, at the same time of day. After a 5-minute acclimatization period, electrocardiogram and respiration were recorded at rest. For validation, average heart rate and RMSSD were assessed over 15 minutes using a validated open-source toolbox. Test-retest agreement was evaluated using intra-class correlation (ICC), and coefficients of variation (CV). Mean heart rate showed high stability (ICC = 0.81, CV = 6%), while RMSSD had lower concordance (ICC = 0.75) and greater variation (CV = 30%). These findings indicate good test-retest agreement for standard HRV features. However, a wide range of methodologies exists for assessing various properties of heart rate dynamics. This database is intended to support other researchers in testing additional HRV metrics to evaluate their reliability in healthy individuals.
Combating COVID-19 and its co-infection by Aspergillus tamarii SP73-EGY using in vitro and in silico Studies
Authors: Abdelsalam Eman , Ibrahim Amal Mosad , El-Rashedy Ahmed A. , Abdel-Aziz Mohamed S. , Kutkat Omnia , EL-Hady Faten K. Abd 
Published: January 2025

AbstractThe COVID-19 pandemic has caused significant mortality and morbidity for millions of people. Severe Acute Respiratory Syndrome-2 (SARS-CoV-2) virus is capable of causing severe and fatal diseases. We evaluated the antiviral properties of Aspergillus tamarii SP73-EGY isolate extract against low pathogenic coronavirus (229E), Adeno-7- and Herpes-2 viruses. The extract showed a high selectivity index (SI = 43.4) and a significant inhibition of 229E (IC50 = 8.205 μg/ml). It was stronger than the drug control, remdesivir (IC50 = 38.2 μg/ml, SI = 7.29). However, the extract showed minimal efficacy against Adeno-7- and Herpes-2-Viruses (IC50 = 22.52, 47.79 μg/ml, and SI = 6.75, 5.08, respectively). It exhibited profound efficacy against the highly pathogenic SARS-CoV-2 (IC50 = 8.306 μg/ml, SI = 42.2). Kojic acid, the primary component of the extract, showed substantial antiviral activity against SARS-CoV-2 (IC50 = 23.4 μg/ml, SI = 5.6), Remdesivir (IC50 = 4.55 μg/ml, SI = 61.45). Therefore, the extract demonstrated the most notable antiviral characteristics against coronavirus infection. Co-infecting microorganisms may contribute to immune system deterioration and airway injury caused by SARS-CoV-2. The extract showed significant efficacy against E. coli and P. aeruginosa, with an inhibition range of 3.5–10 mm at a concentration of 200 mg/ml. A molecular docking study showed that hexadecanoic, Kojic, octanoic acids, and 4(4-Methylbenzylidene)cyclohexane-1,3-dione have stronger binding affinity to the SARS-CoV-2 Mpro than Remdesivir. Molecular dynamics simulations were employed to examine the structural stability and flexibility of these complexes. This confirmed the high binding affinities of Kojic acid and 4(4-Methylbenzylidene)cyclohexane-1,3-dione, thereby proving their potential as novel anti-SARS-CoV-2.
Analysis and prediction of condylar resorption following orthognathic surgery
Authors: Verhelst Pieter-Jan , Janssens Sigrid , Matthews Harold , Begnoni Giacomo , Claes Peter , Shaheen Eman , Peeters Hilde , Politis Constantinus , Jacobs Reinhilde 
Published: January 2025

AbstractCondylar resorption is a feared complication of orthognathic surgery. This study investigated condylar resorption in a cohort of 200 patients This allowed for a powerful update on incidence and risk factors. 9.5% of patients developed resorption. These patients had on average, 17% volume loss with 3.9 mm ramal height loss and 3.1 mm posterior mandibular displacement. 2% of patients had bilateral resorption. Univariable analysis identified a younger age, a bimaxillary + genioplasty procedure, larger mandibular advancements, upward movements of the distal segment, a higher counterclockwise pitch of the distal segment, smaller preoperative condylar volumes and a higher anterior/posterior lower facial height ratio as risk factors on a patient level. Univariable analysis on a condylar level also identified compressive movements of the ramus and a higher mandibular plane angle as risk factors. Using machine learning for the multivariable analysis, the amount of mandibular advancement was the most important predictor for condylar resorption. There were no differences in preoperative mandibular, ramal or condylar shape between patients with or without resorption. These findings suggest condylar resorption may be more common than thought. Identifying risk factors allows surgical plans to be adjusted to reduce the likelihood of resorption, and patients can be more selectively screened postoperatively.
Synthesis and crystal structure of piperidinyl propanenitrile towards the preparation of piperidine based bioactive films for drug delivery applications
Authors: Mohamed-Ezzat Reham A. , Hasanin Mohamed S. , Kariuki Benson M. , Dacrory Sawsan 
Published: January 2025

AbstractCompounds containing the piperidine group are highly attractive as building blocks for designing new drugs. Functionalized piperidines are of significant interest due to their prevalence in the pharmaceutical field. Herein, 3-oxo-3-(piperidin-1-yl) propanenitrile has been synthesized, and piperidine-based sodium alginate/poly(vinyl alcohol) films have been prepared. The polymeric films display potency and potential for application to fight against microbial infections. The films could also help maintain interaction with tissue to ensure the controlled release of therapeutic molecules. Thus, they are promising in developing drug delivery systems essential in the pharmaceutical industry. The structure of the 3-oxo-3-(piperidin-1-yl)propanenitrile was confirmed via spectroscopic and single crystal x-ray diffraction techniques. A homogenous solution of sodium alginate (SA) was used to prepare the film by the casting method in the presence of poly(vinyl alcohol) (PVA) and 3-oxo-3-(piperidin-1-yl)propanenitrile (PPN). The prepared films were characterized physiochemically via FTIR, XRD, and TGA. The film morphology was studied using SEM. The antimicrobial potency of the prepared films was assessed against various species of microorganisms. The physicochemical analysis indicated that the films were bound by chemical and physical bond formation between the cyano group of 3-oxo-3-(piperidin-1-yl)propanenitrile, methylene group of PVA, and the hydroxyl group of SA. The films showed smooth, homogenous surfaces and good mechanical properties. The results revealed that the films are bioactive, as indicated by promising antimicrobial potency against P. aeruginosa, S. aureus, E. coli, B. subtilis, and C. albicans, with high potency as well as moderate activity against A. niger. Polymeric films have promising potential to be utilized in drug delivery applications.
Canagliflozin alleviates acetaminophen-induced renal and hepatic injury in mice by modulating the p-GSK3β/Fyn-kinase/Nrf-2 and p-AMPK-α/STAT-3/SOCS-3 pathways
Authors: Bishr Abeer , El-Mokadem Bassant M. , Gomaa Asmaa A. 
Published: January 2025

AbstractDespite the fact that canagliflozin (Cana), a sodium-glucose cotransporter 2 inhibitor, is an anti-diabetic medication with additional effects on the kidney, there is limited experimental data to deliberate its hepato-reno-protective potentiality. Acetaminophen (APAP) overdose remains one of the prominent contributors to hepato-renal damage. Aim: Our study assessed the novel effect of Cana against APAP-induced toxicities. Main methods: mice were randomized into five groups: negative control, Cana25, APAP, Cana10 + APAP, and Cana25 + APAP. Cana was given for 5 days; a single dose of APAP was injected on the 6th day, followed by the scarification of animals 24 h later. Key findings: Pre-treatment with Cana ameliorated hepatic and renal functions, whereas, on the molecular levels, Cana promoted hepatic/renal P-AMP-activated protein kinase-α/ protein kinase B (p-Akt)/Glycogen synthase kinase (p-GSK3β) protein expression. Alternatively, Cana dampened the expression of STAT-3 and Fyn-kinase genes with a subsequent increase in the contents of suppressor of cytokine signaling (SOCS)-3 and also boosted the contents of the nuclear factor erythroid related factor 2 (Nrf-2)/heme oxygenase (HO)-1/ NADPH quinone oxidoreductase (NQO)-1 axis. The crosstalk between these paths ameliorated the APAP-induced hepatorenal structural alterations. Significance: Cana hepatorenal protective impact was provoked partly through modulating p-AMPK-α /SOCS-3/STAT-3 and GSK3β/Fyn-kinase signaling for its anti-inflammatory and antioxidant effects.
Validation of energy valley optimization for adaptive fuzzy logic controller of DFIG-based wind turbines
Authors: Elnaghi Basem E. , Ismaiel Ahmed M. , El Sayed Abdel-Kader Fathy , Abelwhab M. N. , Mohammed Reham H. 
Published: January 2025

AbstractThis study presents a novel optimization algorithm known as the Energy Valley Optimizer Approach (EVOA) designed to effectively develop six optimal adaptive fuzzy logic controllers (AFLCs) comprising 30 parameters for a grid-tied doubly fed induction generator (DFIG) utilized in wind power plants (WPP). The primary objective of implementing EVOA-based AFLCs is to maximize power extraction from the DFIG in wind energy applications while simultaneously improving dynamic response and minimizing errors during operation. The performance of the EVOA-based AFLCs is thoroughly investigated and benchmarked against alternative optimization techniques, specifically chaotic billiards optimization (C-BO), genetic algorithms (GA), and marine predator algorithm (MPA)-based optimal proportional-integral (PI) controllers. This comparative analysis is crucial in establishing the efficacy of the proposed method. To validate the proposed approach, experimental assessments are conducted using the DSpace DS1104 control board, allowing for real-time application of the control strategies. The results indicate that the EVOA-AFLCs outperform the C-BO-based AFLCs, GA-based AFLCs, and MPA-based optimal PIs in several key performance metrics. Notably, the EVOA-AFLCs exhibit rapid temporal response, a high rate of convergence, reduced peak overshoot, diminished undershoot, and significantly lower steady-state error. The EVOA-AFLC outperforms the C-BO-AFLC and GA-AFLC in terms of efficiency, transient responses, and oscillations. In comparison to the MPA-PI, it improves speed tracking by 86.3%, the GA-AFLC by 56.36%, and the C-BO by 39.3%. Moreover, integral absolute error (IAE) for each controller has been calculated to validate the system wind turbine performance. The EVOA-AFLC outperforms other approaches significantly, achieving a 71.2% reduction in average integral absolute errors compared to the GA-AFLC, 24.4% compared to the C-BO-AFLC, and an impressive 84% compared to the MPA-PI. These findings underscore the potential of the EVOA as a robust and effective optimization tool for enhancing the performance of adaptive fuzzy logic controllers in DFIG-based wind power systems.
Spike reliability is cell type specific and shapes excitation and inhibition in the cortex
Authors: Russo Simone , Stanley Garrett B. , Najafi Farzaneh 
Published: January 2025

AbstractNeurons encode information in the highly variable spiking activity of neuronal populations, so that different repetitions of the same stimulus can generate action potentials that vary significantly in terms of the count and timing. How does spiking variability originate, and does it have a functional purpose? Leveraging large-scale intracellular electrophysiological data, we relate the spiking reliability of cortical neurons in-vitro during the intracellular injection of current resembling synaptic inputs to their morphologic, electrophysiologic, and transcriptomic classes. Our findings demonstrate that parvalbumin+ (PV) interneurons, a subclass of inhibitory neurons, show high reliability compared to other neuronal subclasses, particularly excitatory neurons. Through computational modeling, we predict that the high reliability of PV interneurons allows for strong and precise inhibition in downstream neurons, while the lower reliability of excitatory neurons allows for integrating multiple synaptic inputs leading to a spiking rate code. These findings illuminate how spiking variability in different neuronal classes affect information propagation in the brain, leading to precise inhibition and spiking rate codes.
A secure and energy-efficient routing using coupled ensemble selection approach and optimal type-2 fuzzy logic in WSN
Authors: Ambareesh S. , Chavan Pundalik , Supreeth S. , Nandalike Rajesh , Dayananda P. , Rohith S. 
Published: January 2025

AbstractWireless sensor networks (WSNs) are imperative to a huge range of packages, along with environmental monitoring, healthcare structures, army surveillance, and smart infrastructure, however they’re faced with numerous demanding situations that impede their functionality, including confined strength sources, routing inefficiencies, security vulnerabilities, excessive latency, and the important requirement to keep Quality of Service (QoS). Conventional strategies generally goal particular troubles, like strength optimization or improving QoS, frequently failing to provide a holistic answer that effectively balances more than one crucial elements concurrently. To deal with those challenges, we advocate a novel routing framework that is both steady and power-efficient, leveraging an Improved Type-2 Fuzzy Logic System (IT2FLS) optimized by means of the Reptile Search Algorithm (RSA). This modern framework employs weighted ensemble clustering and matched ensemble choice techniques, facilitating strong cluster formation and resulting in a substantial 98% development in community lifetime, an 80% enhancement in packet delivery ratio (PDR), and a 45% reduction in average power consumption while as compared to current protocols. The IT2FLS model dynamically adapts routing selections by means of assessing key parameters, consisting of dynamic accept as true with factors, node power ranges, course delays, and energy consumption fees, whilst the RSA algorithm exceptional-tunes the bushy common sense club features to make certain most beneficial cluster head choice and reliable multi-hop communication paths. Additionally, our proposed technique complements secure routing by means of efficaciously counteracting the effects of compromised nodes, for this reason maintaining community integrity. Multiple test results show that RSA’s enhanced IT2FLS system consistently outperforms new standards. It reduces end-to-end work by 25% and significantly increases productivity. These findings suggest that this robust routing model not only guarantees efficient data transmission and performance. But it also guarantees the stability of the overall network. This research contributes significantly to the WSN field by providing a comprehensive routing solution that integrates energy conservation, security, and QoS, ultimately extending the lifespan of WSNs and boosting confidence in critical applications, paving the way for implementation scenarios that require secure, low-power, and real-time data transmission.