bluuebunny/crossref_metadata_2025_split huggingface dataset:
Atmospheric ion escape and solar wind deposition as a function of planetary radius
Authors: Hinton P C , Brain D A , Schnepf N R , Jarvinen R , Ramstad R 
Published: September 2024

ABSTRACT
We explore the ability of an unmagnetized planet to retain an atmosphere as a function of its radius. We use a particle-in-cell hybrid code to simulate the global plasma interaction of unmagnetized terrestrial planets at 1 au under average solar wind conditions. We vary the radius of the planet $(R_\mathrm{ p})$ from Mars-sized ($3390 \ \mathrm{km}$) to super-Earth-sized ($9390 \ \mathrm{km}$). We inject hydrogen and oxygen ion outflows from the ionosphere and quantify how the ion escape, recirculation, solar wind deposition, and net atmospheric mass flux vary as a function of planetary radius. We find that as the radius and the corresponding ionospheric outflow rate are varied, the fraction of outflowing $\mathrm{ H^+}$ that escapes remains at $15.5\pm 1.0{{\ \rm per\, cent}}$, while the rest recirculates back towards the planet. The fraction of produced $\mathrm{ O^+}$ that escapes from a Mars-sized planet is $27\pm 1{{\ \rm per\, cent}}$, and decreases to $7\pm 1{{\ \rm per\, cent}}$ for super-Earth, suggesting that smaller planets are less able to retain heavy ions. We find, however, that larger planets have lower solar wind deposition fractions because their bow shocks are at greater distances from the surface of the planet. The ionospheric outflow rate at which mass deposition is equal to mass escape is found to be proportional to $R_\mathrm{ p}^2$. Lastly, we propose that the bulk gyration of the solar wind at the induced magnetosphere can lead to differential escape trajectories of light and heavy ions.
Light-curve analysis and shape models of NEAs 7335, 7822, 154244, and 159402
Authors: Rodríguez Rodríguez Javier , Díez Alonso Enrique , Iglesias Álvarez Santiago , Pérez Fernández Saúl , Buendia Roca Alejandro , Fernández Díaz Julia , Licandro Javier , Alarcon Miguel R , Serra-Ricart Miquel , Pinilla-Alonso Noemi , de Cos Juez Francisco Javier 
Published: September 2024

ABSTRACT
In an attempt to further characterize the near-Earth asteroid (NEA) population, we present 38 new light curves acquired between 2020 September and 2023 November for NEAs (7335) 1989 JA, (7822) 1991 CS, (154244) 2002 KL6, and (159402) 1999 AP10, obtained from observations taken at the Teide Observatory (Tenerife, Spain). With these new observations along with archival data, we computed their first shape models and spin solutions by applying the light-curve inversion method. The obtained rotation periods are in good agreement with those reported in previous works, with improved uncertainties. Additionally, besides the constant period models for (7335) 1989 JA, (7822) 1991 CS, and (159402) 1999 AP10, our results for (154244) 2002 KL6 suggest that it could be affected by a Yarkovsky–O’Keefe–Radzievskii–Paddack acceleration with a value of $\upsilon \simeq -7\times 10^{-9}$ rad d$^{-2}$. This would be one of the first detections of this effect slowing down an asteroid.
Eukaryotic initiation factor 4B is a multi-functional RNA binding protein that regulates histone mRNAs
Authors: Quintas Ana , Harvey Robert F , Horvilleur Emilie , Garland Gavin D , Schmidt Tobias , Kalmar Lajos , Dezi Veronica , Marini Alberto , Fulton Alexander M , Pöyry Tuija A A , Cole Cameron H , Turner Martin , Sawarkar Ritwick , Chapman Michael A , Bushell Martin , Willis Anne E 
Published: September 2024

Abstract
RNA binding proteins drive proliferation and tumorigenesis by regulating the translation and stability of specific subsets of messenger RNAs (mRNAs). We have investigated the role of eukaryotic initiation factor 4B (eIF4B) in this process and identify 10-fold more RNA binding sites for eIF4B in tumour cells from patients with diffuse large B-cell lymphoma compared to control B cells and, using individual-nucleotide resolution UV cross-linking and immunoprecipitation, find that eIF4B binds the entire length of mRNA transcripts. eIF4B stimulates the helicase activity of eIF4A, thereby promoting the unwinding of RNA structure within the 5′ untranslated regions of mRNAs. We have found that, in addition to its well-documented role in mRNA translation, eIF4B additionally interacts with proteins associated with RNA turnover, including UPF1 (up-frameshift protein 1), which plays a key role in histone mRNA degradation at the end of S phase. Consistent with these data, we locate an eIF4B binding site upstream of the stem–loop structure in histone mRNAs and show that decreased eIF4B expression alters histone mRNA turnover and delays cell cycle progression through S phase. Collectively, these data provide insight into how eIF4B promotes tumorigenesis.
The Effect of Chia Seed on Blood Pressure, Body Composition, and Glycemic Control: A GRADE-Assessed Systematic Review and Dose-Response Meta-Analysis of Randomized Controlled Trials
Authors: TaghipourSheshdeh Faranak , Behzadi Mehrdad , Bashiri Sara , Mohammadi-Sartang Mohsen 
Published: September 2024

Abstract

Context
Numerous studies have demonstrated the positive effects on metabolic factors of consuming chia seeds. However, the results of clinical trials have been inconsistent.

Objective
The aim of this study was to conduct a systematic review and meta-analysis of available randomized controlled trials to explore the effects of chia seed consumption on body weight (BW), body composition, blood pressure, and glycemic control.

Data Sources
A comprehensive search was conducted on the Scopus, PubMed, Medline via Ovid, ISI Web of Science, and Scholar Google databases up to August 2023.

Data Extraction
The outcomes of interest included systolic blood pressure (SBP), diastolic blood pressure (DBP), BW, body mass index (BMI), body fat percentage, waist circumference (WC), fasting blood glucose (FBG), and hemoglobin A1c (HbA1c).

Data Analysis
Weighted mean difference (WMD) and 95% CIs were used to determine the effect size.

Results
A total of 8 eligible studies were included in the analysis. The findings revealed a significant reduction in SBP (WMD: −7.19 mmHg; 95% CI, −10.63 to −3.73; P &lt; .001) and DBP (WMD: −6.04 mmHg, 95% CI, −9.58 to −2.49; P = .001). However, no significant effects were observed on BW, body fat percentage, WC, BMI, FBG, and HbA1c. Subgroup analysis indicated that the effect of chia seed on SBP was significant in participants with a baseline SBP of less than 140 mmHg, but the effect was not dependent on the administered dose.

Conclusion
Chia seed consumption has positive effects on SBP and DBP but does not significantly impact BW, body composition, or glycemic parameters. However, the limited amount of data from included studies should be considered as a limitation while interpreting these findings.

Systematic Review Registration
PROSPERO registration no. CRD42023462575.
Phosphorylation of CRYAB Induces a Condensatopathy to Worsen Post-Myocardial Infarction Left Ventricular Remodeling
Authors: Islam Moydul , Rawnsley David R. , Ma Xiucui , Navid Walter , Zhao Chen , Foroughi Layla , Murphy John T. , Navid Honora , Weinheimer Carla J. , Kovacs Attila , Nigro Jessica , Diwan Aaradhya , Chang Ryan , Kumari Minu , Young Martin E. , Razani Babak , Margulies Kenneth B. , Abdellatif Mahmoud , Sedej Simon , Javaheri Ali , Covey Douglas F. , Mani Kartik , Diwan Abhinav 
Published: September 2024

AbstractProtein aggregates are emerging therapeutic targets in rare monogenic causes of cardiomyopathy and amyloid heart disease, but their role in more prevalent heart failure syndromes remains mechanistically unexamined. We observed mis-localization of desmin and sarcomeric proteins to aggregates in human myocardium with ischemic cardiomyopathy and in mouse hearts with post-myocardial infarction ventricular remodeling, mimicking findings of autosomal-dominant cardiomyopathy induced by R120G mutation in the cognate chaperone protein, CRYAB. In both syndromes, we demonstrate increased partitioning of CRYAB phosphorylated on serine-59 to NP40-insoluble aggregate-rich biochemical fraction. While CRYAB undergoes phase separation to form condensates, the phospho-mimetic mutation of serine-59 to aspartate (S59D) in CRYAB mimics R120G-CRYAB mutants with reduced condensate fluidity, formation of protein aggregates and increased cell death. Conversely, changing serine to alanine (phosphorylation-deficient mutation) at position 59 (S59A) restored condensate fluidity, and reduced both R120G-CRYAB aggregates and cell death. In mice, S59D CRYAB knock-in was sufficient to induce desmin mis-localization and myocardial protein aggregates, while S59A CRYAB knock-in rescued left ventricular systolic dysfunction post-myocardial infarction and preserved desmin localization with reduced myocardial protein aggregates. 25-Hydroxycholesterol attenuated CRYAB serine-59 phosphorylation and rescued post-myocardial infarction adverse remodeling. Thus, targeting CRYAB phosphorylation-induced condensatopathy is an attractive strategy to counter ischemic cardiomyopathy.
Electrospun Fiber Surface Roughness Modulates Human Monocyte-Derived Macrophage Phenotype
Authors: Alemifar Aidan , Burnette KaLia , Jandres Bryan , Hurt Samuel , Tse Hubert M. , Robinson Jennifer L. 
Published: September 2024

ABSTRACTInjuries to fibrous connective tissues have very little capacity for self-renewal and exhibit poor healing after injury. Phenotypic shifts in macrophages play a vital role in mediating the healing response, creating an opportunity to design immunomodulatory biomaterials which control macrophage polarization and promote regeneration. In this study, electrospun poly(-caprolactone) fibers with increasing surface roughness (SR) were produced by increasing relative humidity and inducing vapor-induced phase separation during the electrospinning process. The impact of surface roughness on macrophage phenotype was assessed using human monocyte-derived macrophagesin vitroandin vivousing B6.Cg-Tg(Csf1r-EGFP)1Hume/J (MacGreen) mice.In vitroexperiments showed that macrophages cultured on mesh with increasing SR exhibited decreased release of both pro- and anti-inflammatory cytokines potentially driven by increased protein adsorption and biophysical impacts on the cells. Further, increasing SR led to an increase in the expression of the pro-regenerative cell surface marker CD206 relative to the pro-inflammatory marker CD80. Mesh with increasing SR were implanted subcutaneously in MacGreen mice, again showing an increase in the ratio of cells expressing CD206 to those expressing CD80 visualized by immunofluorescence. SR on implanted biomaterials is sufficient to drive macrophage polarization, demonstrating a simple feature to include in biomaterial design to control innate immunity.GRAPHICAL ABSTRACT
Bibliometric Analysis of Circular RNA Cancer Vaccines and Their Emerging Impact
Authors: Das Uddalak , Banerjee Soupayan , Sarkar Meghna 
Published: September 2024

ABSTRACTCircular RNA (circRNA) vaccines are emerging as a revolutionary strategy in cancer immunotherapy, offering novel mechanisms for inducing robust and durable immune responses. Unlike traditional linear mRNA vaccines, circRNAs exhibit exceptional stability, enhanced translational efficiency, and resistance to exonuclease degradation, making them ideal candidates for vaccine development. Recent studies have shown that circRNA vaccines play an important and specialized role in cancer treatment. However, there are currently no relevant bibliometric studies. This study aimed to apply bibliometrics and scientometrics to summarize the knowledge structure and research hotspots regarding the role of circRNA vaccines in cancer. Publications related to circRNA vaccines in cancer were searched on the Scopus database. VOSviewer and Scopus were used to conduct the analyses. This study summarizes the research trends and development of circRNA vaccines for cancer and also a comparative analysis between mRNA cancer vaccine and circRNA cancer vaccine identifying potential areas of focus, innovation and growth. This information will provide a reference for researchers to studying circRNA vaccines against cancer due to its increasing trends over recent times.
Organoid Modeling and Single-Cell Profiling Uncover the Migration Mechanism of Smooth Muscle Cells in Moyamoya Disease
Authors: He Shihao , Zhang Junze , Wang Xilong , Qi Zhen , Zhou Zhenyu , Wang Yanru , Xu Shaoqi , Li Dandan , Ye Xun , Liu Ziqi , Hao Xiaokuan , Zhao Yuanli , Wang Rong 
Published: September 2024

SummaryMoyamoya disease (MMD) is a chronic cerebrovascular disorder characterized by progressive occlusion of the intracranial arteries, resulting in severe ischemic or hemorrhagic stroke. The main characteristic of the affected vessels in MMD is arterial intimal thickening. However, there are no in vitro or in vivo models that can mimic its vascular characteristics. Moreover, the mechanisms underlying the intimal thickening remain unexplained. Here, we generated vascular organoids by differentiating human induced pluripotent stem cell derived from the peripheral blood of MMD patients, thereby creating an organoid model reflecting both the genetic background and characteristics of the affected vessels. Through single-cell sequencing, we found the increased vascular smooth muscle cell (VSMC) proportion and its functional abnormalities in MMD organoids. Proteomics and RNA sequencing identified abnormal TUBA4A and TUBB4B overexpression in both the organoids and patient serum. The following in vitro experiments demonstrated that TUBA4A and TUBB4B promote the contractile-to-synthetic phenotypic switching, migration and proliferation in VSMC. Further experiments identified the GJA1-mediated PI3K/AKT/KLF4 pathway as a key regulating pathway of these phenotypic changes in VSMCs. Our findings demonstrate that the abnormal expression of TUBA4A and TUBB4B in VSMC might be a significant contributor to the intimal thickening in the affected vessels of MMD.
Melastatin subfamily Transient Receptor Potential channels support spermatogenesis in planarian flatworms
Authors: Curry Haley Nicole , Huynh Roger , Rouhana Labib 
Published: September 2024

ABSTRACTThe Transient Receptor Potential superfamily of proteins (TRPs) form cation channels that are abundant in animal sensory systems. Amongst TRPs, the Melastatin-related subfamily (TRPMs) is composed of members that respond to temperature, pH, sex hormones, and various other stimuli. Some TRPMs exhibit enriched expression in gonads of vertebrate and invertebrate species, but their contributions to germline development remain to be determined. We identified twenty-one potential TRPMs in the planarian flatwormSchmidtea mediterraneaand analyzed their anatomical distribution of expression by whole-mountin situhybridization. Enriched expression of two TRPMs (Smed-TRPM-candSmed-TRPM-l) was detected in testis, whereas eight TRPM genes had detectable expression in patterns representative of neuronal and/or sensory cell types. Functional analysis of TRPM homologs by RNA-interference (RNAi) revealed that disruption ofSmed-TRPM-cexpression results in reduced sperm development, indicating a role for this receptor in supporting spermatogenesis.Smed-TRPM-lRNAi did not result in a detectable phenotype, but it increased sperm development deficiencies when combined withSmed-TRPM-cRNAi. Fluorescencein situhybridization revealed expression ofSmed-TRPM-cin early spermatogenic cells within testes, suggesting cell-autonomous regulatory functions in germ cells for this gene. In addition,Smed-TRPM-cRNAi resulted in reduced numbers of presumptive germline stem cell clusters in asexual planarians, suggesting thatSmed-TRPM-csupports establishment, maintenance, and/or expansion of spermatogonial germline stem cells. While further research is needed to identify the factors that trigger Smed-TRPM-c activity, these findings reveal one of few known examples for TRPM function in direct regulation of sperm development.
A Novel Gene Synthesis Platform for Designing Functional Protein Polymers
Authors: Homma Toshimasa , Yamamoto Rie , Ang Lily Zuin Ping , Fehaid Alaa , Ebara Mitsuhiro 
Published: September 2024

AbstractRecombinant protein polymers with repeat sequences of specific amino acids can be regarded as sustainable functional materials that can be designed using genetic engineering. However, synthesizing genes encoding these proteins is significantly time-consuming and labor-intensive owing to the difficulty of using common gene synthesis tools, such as restriction enzymes and PCR primers. To overcome these obstacles, we propose a novel method: seamless cloning of rolling-circle amplicons (SCRCA). This method involves one-pot preparation of repetitive-sequence genes with overlapping ends for cloning, facilitating the easy construction of the desired recombinants. Using SCRCA, we synthesized 10 genes encoding hydrophilic resilin-like and hydrophobic elastin-like repeat units that induce liquid–liquid phase separation. SCRCA shows higher transformation efficiency and better workability than conventional methods, and the time and budget required for SCRCA are comparable to those required for non-repetitive-sequence gene synthesis. Additionally, SCRCA allows the construction of a repeat unit library at a low cost. The library shows considerably higher diversity compared with that of the state-of-the-art method. By combining this library construction with the directed evolution concept, we can rapidly develop an elastin-like protein polymer with a desired function. SCRCA can greatly accelerate research on protein polymers.
Structural Adaptations of HepI Enzymes in Proteobacteria: Insights into Evolutionary Resilience and Functional Dynamics
Authors: Gupta Aayatti Mallick , Butelman June W. , Hassan Bakar A. , Arevalo Philip , Taylor Erika Anne 
Published: September 2024

AbstractSince lipopolysaccharide molecules are highly variable in their structure while also being essential for bacterial cell survival, we hypothesized that enzymes involved in its biosynthesis may exhibit differences that could be used to predict the likelihood of survival in different ecological niches. We examined the sequence variability of orthologues of Heptosyltransferase I (HepI), which is found in all lipopolysaccharide (LPS) containing Gram-negative bacteria. We identified two different sequence motifs within the N-terminal domain of HepI, which correlated with differences in the Lipid A portion of the LPS. Further, we compared the protein structure of HepI fromEscherichia coliwith a structural model we generated that incorporated the alternate sequence motif. Molecular dynamics simulations of these two proteins, recapitulated our findings, that proteins with theE. coli-like sequence motif maintained a larger enzyme active site, while the mutated structural model undergoes rearrangements that lead to a smaller N-terminal active site pocket. This work revealed sequence-structure-function relationships that can be used to determine if a species incorporates a Heptose residue onto Lipid A chains containing one or two 3-deoxy-D-manno-oct-2-ulosonic acid (Kdo) residues. Since research suggests that the number of Kdo residues in LPS impacts the overall immune response to the LPS endotoxin, this work could aid in our understanding of the pathogenic effects of human-bacterial interactions. Understanding the sequence-structural adaptations of HepI enzymes across proteobacteria sheds light on their evolutionary resilience and functional versatility.HighlightsLipopolysaccharide (LPS) structure varies between organismsHeptosytransferase I sequence motifs allow prediction of LPS structural featuresAdaptations of HepI enzymes reveal evolutionary resilience and functional versatility
Revealing a Correlation between Structure andin vitroactivity of mRNA Lipid Nanoparticles
Authors: Chen Xiaoxia , Li Mengrong , Jiang Fan , Hong Liang , Liu Zhuo 
Published: September 2024

AbstractMessenger RNA-containing lipid nanoparticles (mRNA-LNPs) represent a promising platform for disease prevention, cancer immunotherapy, and gene editing, etc. Despite the clinical success of mRNA-LNPs based vaccines in preventing infectious diseases, the relationship between their structure and efficacy remains poorly understood, primarily due to their complex chemical composition. In this study, we generated a series of mRNA-LNPs with varied structural properties andin vitrocellular activities by altering their processing and storage conditions to investigate the structure-activity relationship (SAR) of these nanoparticles. Our findings revealed a moderate anticorrelation between particle size distribution andin vitroactivity, while nanoparticle size and morphology exhibited only weak correlations with efficacy. Notably, the intensity of a characteristic peak, as detected by small angle X-ray scattering (SAXS), demonstrated a strong correlation within vitroactivity. Additionally, the peak width and area were moderately correlated and anticorrelated with activity, respectively. These observations suggest that a more ordered internal structure, as identified by SAXS, is likely associated with enhancedin vitroactivity of mRNA-LNPs. Further analysis using31P nuclear magnetic resonance indicated that lyophilization may induce phase separation of mRNA and lipids within the LNPs, leading to a diminished SAXS peak and reducedin vitroactivity. Overall, our study establishes an SAR for mRNA-LNPs, highlighting that a more ordered internal structure correlates with higher efficacy, which could be instrumental in high-throughput screening of LNP libraries for mRNA loading and monitoring efficacy during storage.SignificanceIn addition to the two mRNA-based vaccines developed for COVID-19, the FDA approved a third mRNA-based vaccine for respiratory syncytial virus in 2024. These vaccines rely on mRNA-containing lipid nanoparticles (mRNA-LNPs), which are also being explored for cancer treatment, gene editing, and antibody production. Despite their promise, the structure-activity relationship of mRNA-LNPs remains inadequately understood, limiting the optimization of lipid formulations, long-term storage, and mechanistic insights. Our study suggests that an ordered internal structure correlates with enhancedin vitroefficacy, consistent with previous findings. We identified the intensity of a peak at ∼0.13 Å-1in small-angle X-ray scattering (SAXS) as a strong indicator of the efficacy. Furthermore, we demonstrated that this correlation aroused from phase separation between mRNA and lipids inside LNPs in the lyophilization process. These insights offer a straightforward method to predictin vitroactivity of mRNA-LNPs with certain formulation and shed light on the mechanisms underlying the loss of mRNA-LNPs’ activity during lyophilization.Table of Content