bluuebunny/crossref_metadata_2025_split huggingface dataset:
EV‐Elute: A universal platform for the enrichment of functional surface marker‐defined extracellular vesicle subpopulations
Authors: de Voogt Willemijn S. , Frunt Rowan , Leandro Raul M. , Triesscheijn Casper S. , Monica Bella , Paspali Ioanna , Tielemans Mark , François Jerney J. J. M. , Seinen Cor W. , de Jong Olivier G. , Kooijmans Sander A. A. 
Published: December 2024

AbstractIntercellular communication via extracellular vesicles (EVs) has been identified as a vital component of a steadily expanding number of physiological and pathological processes. To accommodate these roles, EVs have highly heterogeneous molecular compositions. Given that surface molecules on EVs determine their interactions with their environment, EV functionality likely differs between subpopulations with varying surface compositions. However, it has been technically challenging to examine such functional heterogeneity due to a lack of non‐destructive methods to separate EV subpopulations based on their surface markers. Here, we used the Design‐of‐Experiments (DoE) methodology to optimize a protocol, which we name ‘EV‐Elute’, to elute intact EVs from commercially available Protein G‐coated magnetic beads. We captured EVs from various cell types on these beads using antibodies against CD9, CD63, CD81 and a custom‐made protein binding phosphatidylserine (PS). When applying EV‐Elute, over 70% of bound EVs could be recovered from the beads in a pH‐ and incubation‐time‐dependent fashion. EV subpopulations showed intact integrity by electron microscopy and Proteinase K protection assays and showed uptake patterns similar to whole EV isolates in co‐cultures of peripheral blood mononuclear cells (PBMCs) and endothelial cells. However, in Cas9/sgRNA delivery assays, CD63+ EVs showed a lower capacity to functionally deliver cargo as compared to CD9+, CD81+ and PS+ EVs. Taken together, we developed a novel, easy‐to‐use platform to isolate and functionally compare surface marker‐defined EV subpopulations. This platform does not require specialized equipment or reagents and is universally applicable to any capturing antibody and EV source. Hence, EV‐Elute can open new opportunities to study EV functionality at the subpopulation level.
Association of the nutritional risk index recorded prior to allogeneic hematopoietic cell transplantation with the clinical prognosis in children
Authors: Yonesu Hitomi , Hamada Satoru , Sakiyama Hideki , Kiyuna Shinobu , Oshiro Tokiko , Hyakuna Nobuyuki , Nakanishi Koichi 
Published: December 2024

AbstractIntroductionThe nutritional risk index (NRI), calculated using serum albumin levels and body weight ratio is a known prognostic factor in adult hematopoietic cell transplantation (HCT). However, its usefulness in pediatric HCT settings remains unclear.MethodsIn a retrospective study, we examined pre‐transplant NRI impact on outcomes in 82 pediatric patients undergoing allogeneic HCT.ResultsThe 2‐year non‐relapse mortality (NRM) rate was 7.94% (95% confidence interval [CI], 3.05%–19.8%) and 30.8% (95% CI, 16.7%–52.2%) in the high and low NRI groups, respectively (p = 0.0037).ConclusionWe found that poor nutritional status prior to pediatric HCT led to a worse prognosis, including increased NRM.
Analyzing the Life History of Caimans: The Growth Dynamics of Caiman latirostris From an Osteohistological Approach
Authors: Eugenia Pereyra Maria , Bona Paula , Siroski Pablo , Chinsamy Anusuya 
Published: December 2024

ABSTRACTSkeletochronology and growth dynamics are intensively investigated in vertebrate osteohistology. These techniques are particularly important for interpreting the life history of long‐lived species, such as crocodilians. To understand the longevity, growth dynamics, sexual maturity, and sexual dimorphism of caimans we studied an almost complete ontogenetic series of captive and wild specimens of Caiman latirostris from different localities of Argentina. We identified both cyclical and noncyclical growth marks in juvenile caimans, and we suggest that the latter are associated with environmental stress. By overlapping the growth marks of different individuals, we were able to estimate the minimum age of each specimen. Variations in growth rate are evident in different bones, with the femur and scapula having the highest growth rates, while the fibula and pubis have much slower growth rates. We were able to determine the approximate age of sexual maturity from growth curves deduced from osteohistology, which concurred with those assessed in ecological studies. Additionally based on the growth curves we were able to document different growth dynamics which may be related to sexual dimorphism. This study provides valuable insights into the life history and ecological dynamics of crocodilians, shedding light on their growth patterns, attainment of sexual maturity, and the influence of environmental factors on growth. Furthermore it documents the intraspecific and interelemental osteohistological variation in crocodilians and has direct implications for studies that assess the life history of extinct archosaurs and other sauropsids.
Frog Fibres: What Muscle Architecture Can Tell Us About Anuran Locomotor Function
Authors: Leavey Alice , Richards Christopher T. , Porro Laura B. 
Published: December 2024

ABSTRACTMuscle fibre architecture is an important aspect of anatomy to consider when estimating muscle properties. How fibre architecture varies across species specialising in different locomotor functions is not well understood in anurans, due to difficulties associated with fibre extraction in small animals using traditional methods. This paper presents the first digital analysis of fibre architecture in frogs using an automated fibre‐tracking algorithm and contrast‐enhanced µCT scans. We find differences in hindlimb muscle fibre architecture between frogs specialising in different locomotor modes, as well as examples of many‐to‐one mapping of form to function. The trade‐off between fibre length and muscle physiological cross‐sectional area, and therefore contractile speed, range of motion and muscle force output, differs significantly between jumpers and swimmers, but not walker‐hoppers. Where species place on this functional spectrum of fibre architecture largely depends on the muscle being examined. There is also some evidence that fibre length may be adjusted to increase contractile speed without undertaking the metabolically expensive process of growing and maintaining larger muscles. Finally, we make a detailed outline of the remaining gaps in our understanding of anuran fibre architecture that can now be addressed with this valuable digital method in future research.
Glass Vials Coated with Polymer‐Supported‐Catalysts as Reaction Vessels: Stir, Pour, Rinse and Reuse
Authors: Gayen Arun Kumar , Sardana Harshita , Ramakrishnan S 
Published: December 2024

AbstractLightly crosslinked polymeric gel‐supported catalysts have the potential to retain the recyclability and ease of product isolation of traditional polymer‐supported catalysts, while at the same time, they can provide greater homogeneity of catalytic sites and improved reaction rates, especially in the solvent‐swollen state. In the present study, a strategy is devised to covalently anchor a film of swellable crosslinked polymer onto a suitably surface‐derivatized glass vial, and have utilized this coating to bind to Cu, Pd, and Au catalysts; these coated vials are then utilized for azide‐alkyne click, Suzuki coupling and catalytic reduction reactions, respectively. In all cases, simply stirring the reactant mixture in the vial delivers high yields, and the vials can be rinsed and reused several times with little loss of activity. Several control experiments confirm that the catalysis largely occurred within the coated gel film and is not due to leached‐out metal in the reaction medium. Importantly, this strategy can be very useful, when adapted for critical labeling reactions of biomolecules, wherein reactions are often carried out on very small scales, and ease of product isolation with zero contamination is critical.
Development and Evaluation of Poly(Lactic‐Co‐Glycolic Acid) Encapsulated Betulinic Acid Nanocarrier for Improved Anti‐Tumor Efficacy
Authors: Selepe Cyril Tlou , Dhlamini Khanyisile Sheer , Tshweu Lesego , Kwezi Lusisizwe , Ramalapa Bathabile , Ray Suprakas Sinha 
Published: December 2024

AbstractBetulinic acid (BA) is a promising natural anti‐tumor agent renowned for its activity against various tumor cell types. Despite its favorable profile of low cytotoxicity to normal cells, BA's inherent hydrophobic nature and relatively short systematic half‐life impose hurdles for clinical application. This study introduces a strategy to surmount these obstacles by developing a drug delivery system employing poly(lactic‐co‐glycolic acid) (PLGA)‐encapsulated BA nanoparticles (PLGA‐BA NPs). Rigorous characterization techniques such as dynamic light scattering (DLS), x‐ray diffraction (XRD), and scanning electron microscopy (SEM) analyses are employed to confirm the integrity of the drug within the nanocarriers. The PLGA‐BA NPs demonstrated a mean particle size of 196 ± 6.80 nm. XRD analysis demonstrated the amorphous state of the PLGA‐BA formulation, a characteristic vital for sustained drug release and enhanced bioavailability. The PLGA‐BA NPs exhibited spherical morphology with encapsulation and loading efficiency of 83 ± 9.24% and 7.0 ± 0.4%, respectively, highlighting efficient encapsulation of the drug within the PLGA NPs. In vitro, cytotoxicity assessments demonstrated enhanced anti‐proliferative efficacy against breast and lung tumor cells when utilizing PLGA‐BA NPs in comparison to free BA. This research underlines the potential of employing the developed PLGA‐based nanocarrier to optimize the therapeutic efficacy of BA.
Diclofenac Degradation by Immobilized Chlamydomonas reinhardtii and Scenedesmus obliquus
Authors: Kariyawasam Thamali , Petkovich Martin , Vriens Bas 
Published: December 2024

ABSTRACTDiclofenac (DCF), a commonly used anti‐inflammatory medication, presents environmental concerns due to its presence in water bodies, resistance to conventional wastewater treatment methods, and detection at increasing concentrations (ng/L to µg/L) that highlight DCF as a global emerging pollutant. While microalgae have been effective in degrading DCF in wastewater, immobilization into a matrix offers a promising approach to enhance treatment retention and efficiency. This study aimed to evaluate the efficacy of DCF removal using immobilized freshwater microalgae. Two algal species, Chlamydomonas reinhardtii (Chlamydomonas) and Scenedesmus obliquus (Scenedesmus), were tested for 6 days in both free and immobilized forms to determine if immobilized algae could degrade DCF comparably to free cells. The findings indicate that by Day 3, immobilized Chlamydomonas and Scenedesmus removed 78.0% and 80.1% of DCF, outperforming free‐cell cultures. Mixed cultures demonstrated synergistic effects, with removal amounts of 91.4% for free and 92.3% for immobilized systems. By Day 6, all conditions achieved complete DCF removal (100%). Mechanistic analysis showed 80.0% biodegradation and 20.0% bioaccumulation in free Chlamydomonas and 56.8% biodegradation with 43.2% bioaccumulation in Scenedesmus. Immobilization shifted pathways slightly: in Chlamydomonas, 61.6% of DCF removal occurred via biodegradation, 18.3% via bioaccumulation, and 20.1% via abiotic degradation. For Scenedesmus, immobilization achieved 45.6% biodegradation, 36.6% bioaccumulation, and 17.8% abiotic degradation, enhancing abiotic degradation while maintaining biodegradation efficiency. This research serves as a proof of concept for utilizing immobilized algae in DCF removal and suggests an avenue for improved wastewater treatment of emerging contaminants.
Levels of Bile Acid Metabolism Are Associated With Alterations of Gut Microbes in Hepatocellular Carcinoma
Authors: Yang Zhihao , Zhou Fengqin , Zhan Daqin , Li Pengcheng , Pan Jun 
Published: December 2024

ABSTRACTHepatocellular carcinoma (HCC) is viewed as a metabolism associated disease, and bile acid metabolism is reported to occupy a significant role in the progression of HCC. However, little is known about the association between gut microbes and bile acid metabolism in HCC. Our study was designed to clarify the role of bile acid metabolism and microbiome in the progression of HCC. We investigated the relationship between bile acid metabolism and prognosis and immune cells by mining GSE14520. We studied the microbial profiles and metabolic alterations between the low bile acid group and high bile acid group using 16S rRNA sequencing and metabolomics. HCC patients in the high bile acid metabolism group showed better survival outcome compared with those in the low bile acid metabolism. Immune analysis displayed the close correlation between low bile acid metabolism and infiltration of CD4 + T cells, and the close relationship between high bile acid metabolism and infiltration of CD8 + T cells, macrophage cells in HCC. 16S rRNA sequencing results demonstrated that Blautia, Ruminococcus_gnavus_group, Erysipelotrichaceae_UCG‐003 were mostly enriched in the low bile acid group. Metabolomics of the 109 fecal samples showed that the most enriched metabolites in the low total bile acid group were dihydrocytochalasin B, cucurbic acid and 27‐Norcholestanehexol. Finally, KEGG enrichment analysis identified secondary bile acid biosynthesis and endocrine resistance as the most significant metabolic pathways. High bile acid metabolism was associated with more infiltration of CD8 + T cells, macrophage cells, and better prognosis in HCC. Levels of bile acid were significantly associated with altered gut microbes and metabolites in HCC. Further research related to gut microbes and bile acid metabolism may provide a novel insight into the pathogenesis and therapeutic strategy of HCC.
Acoustic-tagged American Shad utilize historic habitat following dam removal in northern Delaware
Authors: Roday Rachel E. , Park Ian A. , Moore Johnny E. , Feris Serrano Randy J. , Fox Dewayne A. , Hale Edward A. 
Published: December 2024

Abstract

Objective
The anadromous American Shad Alosa sapidissima, a once commercially important species in the mid-Atlantic region, experienced population declines due to overfishing, poor water quality, and impediments to accessing freshwater spawning habitat. Efforts at the regional and national scale substantially addressed the former two obstacles to facilitate population growth, but dam modifications or removal are still ongoing. In 2019, the state of Delaware removed the first barrier to anadromous fish passage on the Brandywine River (a tributary of the Delaware River), Dam 1.

Methods
A total of 24 American Shad were surgically tagged with acoustic transmitters from 2021 to 2022 above recently removed Dam 1 and tracked in the Delaware River estuary and coastal waters of the Atlantic Ocean.

Result
The length of available habitat increased by 1.3 km, and 75.0% of surgically tagged American Shad used historic spawning grounds in the Brandywine River following dam removal. Nine individuals exhibited long-term residency in the Brandywine River from May to June, demonstrating the importance of this newly available habitat to spawning adults. Additionally, one fish returned to the Brandywine River between years, displaying interannual spawning site fidelity and iteroparity. We also observed exploratory behavior of three additional American Shad that exited and returned to the Brandywine River within the same year.

Conclusion
Overall, we document a successful collaborative network via receiver array maintenance to answer questions regarding anadromous fish migration and habitat use following dam removal.
Age, growth, maturity, and mortality of an understudied Gray Snapper fishery from the north-central Gulf of Mexico
Authors: Kim Edward S. M. , McDonald Justin C. , Muñoz-Abril Laia , Drymon J. Marcus , Albins Mark A. , Powers Sean P. 
Published: December 2024

Abstract

Objective
Gray Snapper Lutjanus griseus constitute a significant recreational fishery and minor commercial fishery throughout the Gulf of Mexico. The overall stock appears healthy based on the results of the most recent assessment; in fact, shifting climate conditions have led to range expansions and subsequent population growth in the north-central Gulf of Mexico, a region for which the full suite of basic biological data is currently lacking for this species. This work presents the results of a comprehensive study on the age, growth, maturity, and mortality of Gray Snapper in Alabama and Mississippi waters.

Methods
From 2011 to 2021, otoliths (n = 886) and gonads (n = 364) were sampled and processed according to standard microscopic techniques. Age data were used to fit three separate growth functions and derive estimates of total, natural, and fishing mortality, while testes and ovaries were categorized by reproductive phase to determine maturity at length and age.

Result
Ages ranged from 0 to 27 years, representing one of the most comprehensive collections across published studies to date. Sex-specific growth curves constructed using the von Bertalanffy growth function were preferred over the Gompertz and logistic models based on Akaike information criterion and suggest that males reach a higher mean asymptotic length Lt=731.521−e−0.15t+1.34 than females Lt=704.281−e−0.14t+1.62. Based on histological analyses, we estimate total length at 50% maturity to be 181 mm for males and 273 mm for females and total length at 90% maturity to be 215 mm for males and 354 mm for females. We estimate the age at 50% maturity to be &lt;1.0 year for males and 2.0 years for females and the age at 90% maturity to be 1.4 years for males and 3.6 years for females. Mortality rates calculated using preferred estimators (Z = 0.30–0.38; M = 0.26; F = 0.04–0.12) indicate relatively low levels of exploitation in the north-central Gulf of Mexico, with full recruitment to the fishery occurring at age 4.

Conclusion
Based on these results, the Gray Snapper population in the north-central Gulf of Mexico is characterized by a relatively unexploited age structure with moderate longevity that has been subject to minimal fishing pressure. The findings from this study introduce new regional data for incorporation into assessments and provide an informed basis for future management decisions in this fishery.
Association between the Amplification Parameters of the α‐Synuclein Seed Amplification Assay and Clinical and Genetic Subtypes of Parkinson's Disease
Authors: Grillo Piergiorgio , Concha‐Marambio Luis , Pisani Antonio , Riboldi Giulietta Maria , Kang Un Jung 
Published: December 2024

AbstractBackgroundα‐Synuclein seed amplification assay on cerebrospinal fluid (CSF‐αSyn‐SAA) has shown high accuracy for Parkinson's disease (PD) diagnosis. The analysis of CSF‐αSyn‐SAA parameters may provide useful insight to dissect the heterogeneity of synucleinopathies.ObjectiveTo assess differences in CSF‐αSyn‐SAA amplification parameters in participants with PD stratified by rapid eye movement (REM) sleep behavior disorder (RBD), dysautonomia, GBA, and LRRK2 variants.MethodsClinical and CSF‐αSyn‐SAA data from the Parkinson's Progression Marker Initiative dataset were used. CSF‐αSyn‐SAA parameters included maximum fluorescence (Fmax), time to reach 50% of Fmax (T50), time to threshold (TTT), slope, and area under the curve (AUC). Sporadic PD (n = 371) was stratified according to RBD and dysautonomia (DysA) symptoms. Genetic PD included carriers of pathogenic variants of GBA (GBA‐PD, n = 52) and LRRK2 (LRRK2‐PD, n = 124) gene.ResultsCSF‐αSyn‐SAA was positive in 77% of LRRK2‐PD, 92.3% of GBA‐PD, and 93.8% of sporadic PD. The LRRK2‐PD cohort showed longer T50 and TTT, and smaller AUC than GBA‐PD (P = 0.029, P = 0.029, P = 0.016, respectively) and sporadic PD (P = 0.034, P = 0.033, P = 0.014, respectively). In the sporadic cohort, CSF‐αSyn‐SAA parameters were similar between PD with (n = 157) and without (n = 190) RBD, whereas participants with DysA (n = 193) presented shorter T50 (P = 0.026) and larger AUC (P = 0.029) than those without (n = 150).ConclusionCSF‐αSyn‐SAA parameters vary across genetic and non‐genetic PD subtypes at the group level. These differences are mostly driven by the presence of LRRK2 variants and DysA. Significant overlaps in the amplification parameter values exist between groups and limit their use at the individual level. Further studies are necessary to understand the mechanisms of CSF‐αSyn‐SAA parameter differences. © 2024 International Parkinson and Movement Disorder Society.
Protein Binding Site Representation in Latent Space
Authors: Lohmann Frederieke , Allenspach Stephan , Atz Kenneth , Schiebroek Carl C. G. , Hiss Jan A. , Schneider Gisbert 
Published: December 2024

AbstractInterpretability and reliability of deep learning models are important for computer‐based drug discovery. Aiming to understand feature perception by such a model, we investigate a graph neural network for affinity prediction of protein‐ligand complexes. We assess a latent representation of ligand binding sites and investigate underlying geometric structure in this latent space and its relation to protein function. We introduce an automated computational pipeline for dimensionality reduction, clustering, hypothesis testing, and visualization of latent space. The results indicate that the learned protein latent space is inherently structured and not randomly distributed. Several of the identified protein binding site clusters in latent space correspond to functional protein families. Ligand size was found to be a determinant of cluster geometry. The computational pipeline proved applicable to latent space analysis and interpretation and can be adapted to work for different datasets and deep learning models.
Molecular evolution and interaction of ROS with ion transport for plant abiotic stresses
Authors: Yu Hanxia , Xiao Haoyan , Abou‐Elwafa Salah Fatouh , Qiao Yabei , Chen Lily , Alshehri Mohammed Ali , Wu Yusen , Jiang Wei , Tan Wenbing 
Published: December 2024

AbstractReactive oxygen species (ROS) serve as crucial signaling molecules in plants, enabling rapid responses to environmental stresses such as abiotic factors. ROS production primarily stems from the activation of enzymes such as nicotinamide adenine dinucleotide phosphate (NADPH) oxidases and peroxidases, as well as disruptions in the respiratory and photosynthetic electron transport chains. This oxidative stress triggers signaling pathways that involve in calcium ion (Ca2+) influx across cell membranes, altering ionic conductance. ROS encompass hydroxyl radicals (OH•) and hydrogen peroxide (H2O2), which activate hyperpolarization‐activated Ca2+ channels and influence ion transport dynamics. Our review focuses on the mechanisms driving ROS generation and ion transport during plant responses to abiotic stress. We explore the regulation, characteristics, and potential structures of ROS‐activated ion channels in plants. Specifically, we examine the molecular responses and evolutionary adaptations of Shaker‐type K+ channels (AKT/KAT/GORK/SKOR) under stress conditions. Comparative genetic analyses highlight the conservation of these channels and other ROS‐regulated proteins (e.g., MDHAR, POX, and RBOH), suggesting their essential roles in plant to adapt to diverse stresses. This study underscores the significance of ROS‐regulated proteins in plant stress responses, advocating for further research to elucidate their fundamental roles.