bluuebunny/crossref_metadata_2025_split huggingface dataset:
Results of the Latin American Pediatric Oncology Group (GALOP‐2011) Trial for Patients With Localized Ewing Sarcoma: A Multicentric Study of Interval‐Compressed Multiagent Chemotherapy
Authors: Gregianin Lauro José , Rose Adriana , Villarroel Milena , Almeida Maria Tereza , Siqueira Laurice , Salgado Carmen , da Costa Gildene Alves , Castillo Luis , Santos Pestilho Julie Francine Cerutti , Brunetto Algemir Lunardi ,   GALOP Latin American Pediatric Oncology Group Ewing Sarcoma Investigators
Published: January 2025

ABSTRACTBackgroundGALOP investigators developed a prospective cooperative protocol for localized Ewing sarcoma (ES) incorporating interval‐compressed chemotherapy (VDC/IE, vincristine, doxorubicin, cyclophosphamide/ifosfamide and etoposide). After completing conventional treatment, patients were randomized to 1 year of metronomic chemotherapy (vinblastine and cyclophosphamide).MethodsPhase III randomized prospective trial. Induction consisted of six alternating cycles of VDC/IE every 14 days, followed by local control, and eight cycles of consolidation every 21 days. After consolidation, patients were randomized 1:1 to metronomic chemotherapy or stop treatment, balanced by age (>/< 14 years‐old), sex (M/F), site (pelvic/non‐pelvic), and size (>/< 8 cm). The results of randomization will be published elsewhere with longer follow‐up.ResultsBetween 2011 and 2019, 315 patients (59.7% male, median age 11.0 years) were recruited across 34 centers in Argentina, Brazil, Chile, and Uruguay. The most frequent localizations were axial (45.1%), extremity (38.1%), and pelvic (16.8%). The median time interval between cycles was 19 and 22 days at induction and consolidation, respectively. There were no unexpected toxicity or toxic deaths related to interval compression. The overall response rate post‐induction was 81.6%. Local treatment with surgery (50.8%), radiotherapy (19.7%), or a combination (26%) was performed in 304 (96.5%) patients. With a median follow‐up of 50 months (range: 1.67–121.7), the 5‐year overall and event‐free survivals were 68.6% (SE: 0.030) and 63.7% (SE: 0.029), respectively.ConclusionImplementation of a multi‐institutional protocol with the strategy of interval‐compressed induction for ES in South America was feasible with favorable results. This success is attributed to rigorous protocol adherence, extensive educational efforts, and a strong emphasis on data quality maintenance, demonstrating a reproducible model for countries with similar resource limitations.
The Significant Effects of Threshold Selection for Advancing Nitrogen Use Efficiency in Whole Genome of Bread Wheat
Authors: Sadeqi Mohammad Bahman , Ballvora Agim , Dadshani Said , Siddiqui Md. Nurealam , Kamruzzaman Mohammad , Koua Ahossi Patrice , Léon Jens 
Published: January 2025

ABSTRACTCurrently in wheat breeding, genome wide association studies (GWAS) have successfully revealed the genetic basis of complex traits such as nitrogen use efficiency (NUE) and its biological processes. In the GWAS model, thresholding is common strategy to indicate deviation of expected range of p‐value(s), and it can be used to find the distribution of true positive associations under or over of test statistics. Therefore, the threshold plays a critical role to identify reliable and significant associations in wide genome, while the proportion of false positive results is relatively low. The problem of multiple comparisons arises when a statistical analysis involves multiple simultaneous statistical tests, each of them has the potential to be a discovery. There are several ways to address this problem, including the family‐wise error rate and false discovery rate (FDR), raw and adjusted p‐value(s), consideration of threshold coherence and consonance, and the properties of proportional hypothesis tests in the threshold definition. We encountered some limitations in the definition of FDR threshold, particularly in the upper bounds of linear and nonlinear approaches. We emphasize that empirical null distributions based on permutation test can be useful when the assumption of linear or parametric FDR approaches do not hold. Nevertheless, we believe that it is necessary to utilize modern statistical optimization techniques to evaluate the stability and performance of our results and to select significant FDR threshold. By incorporating the neural network algorithm, it is possible to improve the reliability of FDR threshold and increase the probability of identifying true genetic associations while minimizing the risk of false positives in GWAS results.
LEA_4 motifs function alone and in conjunction with synergistic cosolutes to protect a labile enzyme during desiccation
Authors: Nicholson Vincent , Nguyen Kenny , Gollub Edith , McCoy Mary , Yu Feng , Holehouse Alex S. , Sukenik Shahar , Boothby Thomas C. 
Published: January 2025

AbstractOrganisms from all kingdoms of life depend on Late Embryogenesis Abundant (LEA) proteins to survive desiccation. LEA proteins are divided into broad families distinguished by the presence of family‐specific motif sequences. The LEA_4 family, characterized by 11‐residue motifs, plays a crucial role in the desiccation tolerance of numerous species. However, the role of these motifs in the function of LEA_4 proteins is unclear, with some studies finding that they recapitulate the function of full‐length LEA_4 proteins in vivo, and other studies finding the opposite result. In this study, we characterize the ability of LEA_4 motifs to protect a desiccation‐sensitive enzyme, citrate synthase (CS), from loss of function during desiccation. We show here that LEA_4 motifs not only prevent the loss of function of CS during desiccation but also that they can do so more robustly via synergistically interactions with cosolutes. Our analysis further suggests that cosolutes induce synergy with LEA_4 motifs in a manner that correlates with transfer free energy. This research advances our understanding of LEA_4 proteins by demonstrating that during desiccation their motifs can protect specific clients to varying degrees and that their protective capacity is modulated by their chemical environment. Our findings extend beyond the realm of desiccation tolerance, offering insights into the interplay between IDPs and cosolutes. By investigating the function of LEA_4 motifs, we highlight broader strategies for understanding protein stability and function.
Human recombinant tyrosinase destabilization caused by the double mutation R217Q/R402Q
Authors: Toay Sarah , Sheri Narin , MacDonald Ian , Sergeev Yuri V. 
Published: January 2025

AbstractOculocutaneous albinism is an autosomal recessive inherited disorder associated with mutations in the TYR gene. A single missense change in the tyrosinase (Tyr) could result in partial or complete loss of catalytic activity. The effect of two genetic mutations in the same Tyr as the molecule is less studied. Here, we study single mutation variants, R217Q, R402Q, and a double mutant variant, R217Q/R402Q, to establish a link between alterations at the level of the atomic model of the protein and the disease phenotype. Human recombinant intra‐melanosomal Tyr domains of Tyr and three mutant variants were expressed in T. ni. Larvae were purified using the combination of IMAC and SEC, and diphenolase activities were measured. The Tyr homology model was equilibrated using 100 ns molecular dynamics and analyzed using computational methods. The purified R217Q and R217Q/R402Q variants show decreased catalytic activities compared to those of the Tyr and R402Q variants. The R217Q/R402Q variant has the lowest protein activity and is significantly reduced.
AFFIPred: AlphaFold2 structure‐based Functional Impact Prediction of missense variations
Authors: Pir Mustafa S , Timucin Emel 
Published: January 2025

AbstractProtein structure holds immense potential for pathogenicity prediction, albeit structure‐based predictors are limited compared to the sequence‐based counterparts due to the “structure knowledge gap” between large number of available protein sequences and relatively limited number of structures. Leveraging the highly accurate protein structures predicted by AlphaFold2 (AF2), we introduce AFFIPred, an ensemble machine learning classifier that combines sequence and AF2‐based structural characteristics to predict missense variant pathogenicity. Based on the assessments on unseen datasets, AFFIPred reached a comparable level of performance with the state‐of‐the‐art predictors such as AlphaMissense. We also showed that the recruitment of AF2 structures that are full‐length and represent the unbound states ensures more precise SASA calculations compared to the recruitment of experimental structures. In line with the completeness of the AF2 structures, their use provide a more comprehensive view of the structural characteristics of the missense variation datasets by capturing all variants. AFFIPred maintains high‐level accuracy without the limitations of PDB‐based classifiers. AFFIPred has predicted over 210 million variations of the human proteome, which are accessible at https://affipred.timucinlab.com/.
AggNet: Advancing protein aggregation analysis through deep learning and protein language model
Authors: He Wenjia , Xu Xiaopeng , Li Haoyang , Zhou Juexiao , Gao Xin 
Published: January 2025

AbstractProtein aggregation is critical to various biological and pathological processes. Besides, it is also an important property in biotherapeutic development. However, experimental methods to profile protein aggregation are costly and labor‐intensive, driving the need for more efficient computational alternatives. In this study, we introduce “AggNet,” a novel deep learning framework based on the protein language model ESM2 and AlphaFold2, which utilizes physicochemical, evolutionary, and structural information to discriminate amyloid and non‐amyloid peptides and identify aggregation‐prone regions (APRs) in diverse proteins. Benchmark comparisons show that AggNet outperforms existing methods and achieves state‐of‐the‐art performance on protein aggregation prediction. Also, the predictive ability of AggNet is stable across proteins with different secondary structures. Feature analysis and visualizations prove that the model effectively captures peptides' physicochemical properties effectively, thereby offering enhanced interpretability. Further validation through a case study on MEDI1912 confirms AggNet's practical utility in analyzing protein aggregation and guiding mutation for aggregation mitigation. This study enhances computational tools for predicting protein aggregation and highlights the potential of AggNet in protein engineering. Finally, to improve the accessibility of AggNet, the source code can be accessed at: https://github.com/Hill-Wenka/AggNet.
The multifaceted role of XCL1 in health and disease
Authors: Syed Muhammed , Dishman Acacia F. , Volkman Brian F. , Walker Tara L. 
Published: January 2025

AbstractThe chemokine XC motif chemokine ligand 1 (XCL1) is an unusually specialized member of a conserved family of around 50 small, secreted proteins that are best known for their ability to stimulate the directional migration of cells. All chemokines adopt a very similar folded structure that binds a specific G protein‐coupled receptor (GPCR), and most chemokines bind extracellular matrix glycosaminoglycans, often in a dimeric or oligomeric form. Owing in part to the lack of a disulfide bond that is conserved in all other chemokines, XCL1 interconverts between two distinct structures with distinct functions. One XCL1 fold resembles the structure of all other chemokines (chemokine fold), while the other does not (alternate fold). The chemokine fold of XCL1 displays high affinity for the GPCR XCR1, while the alternative fold binds GAGs and exhibits antimicrobial activity. Although the canonical role of XCL1 as a CD8+ dendritic cell chemoattractant was defined more than a decade ago, the misconception that XCL1 is a lymphocyte‐specific chemoattractant still prevails in the recent literature. This review aims to highlight the structure‐guided functions of XCL1 and reclarify its immunological role. In addition, the implications of this metamorphic chemokine in vaccine development and emerging functions in the nervous system will be explored.
Citrullination at the N‐terminal region of MDM2 by the PADI4 enzyme
Authors: Neira José L. , Rizzuti Bruno , Palomino‐Schätzlein Martina , Rejas Virginia , Abian Olga , Velazquez‐Campoy Adrian 
Published: January 2025

AbstractPADI4 is one of the human isoforms of a family of enzymes involved in the conversion of arginine to citrulline. MDM2 is an E3 ubiquitin ligase that is critical for degradation of the tumor suppressor gene p53. We have previously shown that there is an interaction between MDM2 and PADI4 in cellulo, and that such interaction occurs through the N‐terminal region of MDM2, N‐MDM2, and in particular through residues Thr26, Val28, Phe91, and Lys98. Here, by using a “divide‐and‐conquer” approach, we have designed and synthesized peptides comprising these two polypeptide stretches (residues Ala21–Lys36, and Lys94–Val108), either in the wild‐type species or in their citrullinated versions. Some of the citrullinated peptides were aggregation‐prone, as suggested by DOSY‐NMR experiments, but the wild‐type versions of both fragments were monomeric in solution. We found out that wild‐type and modified peptides were disordered in all cases, as also tested by far‐UV circular dichroism (CD), and citrullination mainly affected the NMR chemical shifts of adjacent residues. Isothermal titration calorimetry (ITC) in the absence and presence of GSK484, an enzymatic PADI4 inhibitor, indicated that this compound blocked binding of the peptides to the enzyme. Binding to the active site of the N‐MDM2 fragments was also confirmed by in silico experiments. The affinities of PADI4 for the wild‐type peptides were more favorable than those of the corresponding citrullinated ones, but all measured values were within the micromolar range, indicating that there were no major variations in the thermodynamics of binding due to sequence effects. The kinetic dissociation rates, koff, measured by biolayer interferometry (BLI), were always one‐order of magnitude faster for the citrullinated peptides than for the wild‐type ones. Taken together, all these findings indicate that MDM2 is a substrate for PADI4 and is prone to citrullination in the identified (and specific) positions of its N‐terminal region.
Cripto‐1 acts as a molecular bridge linking nodal to ALK4 via distinct structural domains
Authors: Chu Kit‐Yee , Crawford Amberly N. , Krah Bradon S. , Thamilselvan Vijayalakshmi , Malik Anjali , Aitas Nina A. , Martinez‐Hackert Erik 
Published: January 2025

AbstractThe TGF‐β family ligand Nodal is an essential regulator of embryonic development, orchestrating key processes such as germ layer specification and body axis formation through activation of SMAD2/3‐mediated signaling. Significantly, this activation requires the co‐receptor Cripto‐1. However, despite their essential roles in embryogenesis, the molecular mechanism through which Cripto‐1 enables Nodal to activate the SMAD2/3 pathway has remained elusive. Intriguingly, Cripto‐1 also has been shown to antagonize other TGF‐β family ligands, raising questions about its diverse functions. To clarify how Cripto‐1 modulates TGF‐β signaling, we integrated AlphaFold3 modeling, surface plasmon resonance (SPR)‐based protein–protein interaction analysis, domain‐specific anti‐Cripto‐1 antibodies, and functional studies in NTERA‐2 cells. In contrast to canonical TGF‐β signaling, where ligands bridge type I and type II receptors for activation, Nodal, bound to the type II receptor, utilizes Cripto‐1 to recruit the type I receptor ALK4, forming a unique ternary complex for SMAD2/3 activation. Our molecular characterization of Cripto‐1‐mediated Nodal signaling clarifies the unique role of this enigmatic co‐receptor and advances our understanding of signaling regulation within the TGF‐β family. These insights have potential implications for both developmental biology and cancer research.
Multiscale Three‐Dimensional Evaluation and Analysis of Murine Lung Vasculature From Macro‐ to Micro‐Structural Level
Authors: Tielemans Birger , Marain Nora F. , Kerstens Axelle , Peredo Nicolas , Coll‐Lladó Montserrat , Gritti Nicola , de Villemagne Perrine , Dorval Paul , Geudens Vincent , Orlitová Michaela , Munck Sebastian , Leszczyński Bartosz , Swoger Jim , Velde Greetje Vande 
Published: January 2025

ABSTRACTThe pulmonary vasculature plays a pivotal role in the development and progress of chronic lung diseases. Due to limitations of conventional two‐dimensional histological methods, the complexity and the detailed anatomy of the lung blood circulation might be overlooked. In this study, we demonstrate the practical use of optical serial block face imaging (SBFI), ex vivo microcomputed tomography (micro‐CT), and nondestructive optical tomography for visualization and quantification of the pulmonary circulation's 3D architecture from macro‐ to micro‐structural levels in murine lung samples. We demonstrate that SBFI can provide rapid, cost‐effective, and label‐free visualization of mouse lung macrostructures and large pulmonary vessels. Micro‐CT offers high‐resolution imaging and captures microvascular and (pre)capillary structures, with microstructural quantification. Optical microscopy techniques such as optical projection tomography (OPT) and light sheet fluorescence microscopy, allows noninvasive, mesoscopic imaging of optically cleared mouse lungs, still enabling 3D microscopic reconstruction down to the precapillary level. By integrating SBFI, micro‐CT, and nondestructive optical microscopy, we provide a framework for detailed and 3D understanding of the pulmonary circulation, with emphasis on vascular pruning and rarefaction. Our study showcases the applicability and complementarity of these techniques for organ‐level vascular imaging, offering researchers flexibility in selecting the optimal approach based on their specific requirements. In conclusion, we propose 3D‐directed approaches for a detailed whole‐organ view on the pulmonary vasculature in health and disease, to advance our current knowledge of diseases affecting the pulmonary vasculature.
Theoretical Study of Halogen Anion Batteries With Ultra‐Thin InSe
Authors: Wei Xin , Liu Fengjun , Zhu Mengyu , Wang Lin , Sha Maolin 
Published: January 2025

ABSTRACTWe systematically explored the adsorption, diffusion, thermodynamics stability, and electrochemical performance of halogen anions (F−, Cl−, Br−, I−) on monolayer InSe using first‐principles calculations. F−, due to its strong electronegativity, has a destructive effect on the surface. The rank of the adsorption ability of other three anions is Cl− > Br− > I− according to the value of adsorption energy, which is agreement with their electronegativity strength. It was found that the halogen anions exhibited excellent diffusion performance with low diffusion energy barriers. Cl− can adsorb up to three layer showing an excellent theoretical capacity of 415 mA h g−1, while Br− and I− cannot obtain a stable structure when the coverage exceeds 1 and (2/3) layer. In summary, this study evaluates a prospective electrode material and establishes a theoretical foundation for the development of novel rechargeable batteries.
Establishment of a 3D spheroid culture system to evaluate the responsiveness of uterine leiomyoma cells to female hormones
Authors: Sakai Takahiro , Sato Shun , Tamehisa Tetsuro , Takasaki Hitomi , Kajimura Takuya , Tamura Isao , Sugino Norihiro 
Published: January 2025

AbstractPurposeUterine leiomyomas (ULMs) are classified into those with and without MED12 mutations (MED12m(+) and MED12m(−), respectively). This study was undertaken to establish a culture system to evaluate the effect of female hormones on the growth of ULM cells in each ULM subtype.MethodsULM cells isolated from MED12m(+) or MED12m(−) tissues were cultured in a monolayer for 7 days with four hormone treatments: estrogen (E) and progesterone (P) (E + P), E only (E), P only (P), and medium only (CTRL). They were also cultured in a 3D spheroid culture system with the above four treatments and a fifth treatment: E + P + selective progesterone receptor modulator (E + P + SPRM). The hormonal effects were evaluated based on cell number, spheroid size, and histology.ResultsIn the monolayer cultures, female hormones did not cause the proliferation of ULM cells of either subtype. In the spheroid cultures, spheroid sizes for both subtypes were significantly larger with the E + P and P treatments than with the CTRL and E treatments and were comparable in the E and E + P + SPRM treatments. Histological staining showed that collagen fibers were present only in the spheroids of the P‐treated groups of MED12m(+).ConclusionWe established a 3D spheroid culture system to evaluate the effects of female hormones on ULM cells.
Embryologist staffing in assisted reproductive technology laboratories: An international comparative review
Authors: Shirasawa Hiromitsu , Terada Yukihiro 
Published: January 2025

AbstractBackgroundEmbryologists are crucial in assisted reproductive technology (ART), yet their duties, education, and licensing requirements vary significantly across countries, complicating the determination of optimal staffing levels in ART laboratories. With anticipated advancements such as automation in ART laboratories, this review comprehensively analyzes factors necessary for appropriate future staffing.Main FindingsA comprehensive literature search was conducted using PubMed to identify relevant articles up to July 2024, employing keywords such as “embryologist,” “staffing,” and “certification.” Articles were evaluated for content related to laboratory operations, and guidelines from five organizations regarding licensing and education were compared.ResultsThe review revealed significant international differences in embryologist certification, duties, and staffing recommendations. These disparities, along with the integration of advanced ART technologies and regulatory requirements, significantly impact future staffing needs in ART laboratories.ConclusionThe definitions of an ART cycle and required staffing levels vary across organizations, influenced by the certification and duties of embryologists in different countries. Adequate embryologist staffing is essential for ensuring laboratory quality control and impacting patient ART outcomes. As new technologies and automation reshape laboratory workflows, collaborative efforts among organizations, countries, and embryologist associations are essential for developing comprehensive educational curricula and determining appropriate staffing levels.
Reading Fiction and Psychological Well‐being During Older Adulthood: Positive Affect, Connection and Personal Growth
Authors: Currie Nicola K. , Wilkinson Katherine , McGeown Sarah 
Published: January 2025

AbstractThe relationship between reading and well‐being is gaining increasing interest among those working in research, policy and practice, as we seek to better understand if, and how, reading books supports wellbeing. To date, the majority of research has focused on children and young people, neglecting to consider the well‐being benefits that reading books may have later in life. Drawing upon in‐depth interviews with 15 older adults (aged 63–83) from the UK, we provide novel insights into how reading fiction supports feelings of positive affect (emotions elicited by, and influencing, reading experiences), connection (to fictional characters, settings, and authors, in addition to real‐life others) and personal growth (lifelong reflection, empathy and enhanced understanding of others, and improved knowledge and communication). This article provides much needed nuanced insights into the role of fiction book reading later in life. Implications for practice and future research directions are suggested.