bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spatial and Temporal Heterogeneity of Martian Tropical Water Ice Through Analysis of Radial and Layered Ejecta Craters
Authors: Kirchoff Michelle R. , Grimm Robert E. , Riggs Jamie D. 
Published: November 2024

AbstractMartian layered ejecta craters are theorized to form by impacting into an ice‐rich crust. The inference that some equatorial layered ejecta craters are Amazonian indicates that ice has persisted in the tropics. However, the detailed spatial and temporal distribution and evolution of this ice remain unknown, which is critical to constraining Mars' global water cycle and climate change over eons. Here we estimate absolute model formation ages for layered and radial (ballistic) ejecta craters to constrain the spatial and temporal distribution of equatorial ice. The assumption is that radial ejecta form where volatiles are not present in significant quantities. Ages are derived from the density of smaller craters superposed on the ejecta blankets. We examined 73 craters in a 30° × 30° area centered at 15°S, 355°E, with 44 layered and 29 radial ejecta. Layered and radial ejecta craters are mixed over distances comparable to their diameters, which represents an unreasonably short length scale for ground‐ice emplacement. This, along with the lack of trend with age, supports the suggestion that intermittent low‐latitude surface ice—from excursions to high obliquity—could be responsible. Analysis also suggests an increasing proportion of layered ejecta craters with decreasing diameter for those older than 3.4 Ga. This trend would support the hypothesis of more ice being available in early martian history. Conversely, this could indicate that “armoring” preferentially preserves layered ejecta relative to radial ejecta.
Towards a new taxonomy of preterm birth
Authors: Stevenson David K. , Chang Alan L. , Wong Ronald J. , Reiss Jonathan D. , Gaudillière Brice , Sylvester Karl G. , Ling Xuefeng B. , Angst Martin S. , Shaw Gary M. , Katz Michael , Aghaeepour Nima , Marić Ivana 
Published: November 2024

AbstractDisease categories traditionally reflect a historical clustering of clinical phenotypes based on biologic and nonbiologic features. Multiomics approaches have striven to identify signatures to develop individualized categorizations through tests and/or therapies for ‘personalized’ medicine. Precision health classifies clinical syndromes into endotype clusters based on novel technological advancements, which can reveal insights into the etiologies of phenotypical syndromes. A new taxonomy of preterm birth should be considered in this context, as not all preterm infants of similar gestational ages are the same because most have different biologic vulnerabilities and hence different health trajectories. Even the choice of interventions may affect observed clinical conditions. Thus, a new taxonomy of prematurity would help to advance the field of neonatology, but also obstetrics and perinatology by adopting anticipatory and more targeted approaches to the care of preterm infants with the intent of preventing and treating some of the most common newborn pathologic conditions.
Automating life science labs at the single-cell level through precise ultrasonic liquid sample ejection: PULSE
Authors: Zhang Peiran , Tian Zhenhua , Jin Ke , Yang Kaichun , Collyer Wesley , Rufo Joseph , Upreti Neil , Dong Xianjun , Lee Luke P. , Huang Tony Jun 
Published: November 2024

AbstractLaboratory automation technologies have revolutionized biomedical research. However, the availability of automation solutions at the single-cell level remains scarce, primarily owing to the inherent challenges of handling cells with such small dimensions in a precise, biocompatible manner. Here, we present a single-cell-level laboratory automation solution that configures various experiments onto standardized, microscale test-tube matrices via our precise ultrasonic liquid sample ejection technology, known as PULSE. PULSE enables the transformation of titer plates into microdroplet arrays by printing nanodrops and single cells acoustically in a programmable, scalable, and biocompatible manner. Unlike pipetting robots, PULSE enables researchers to conduct biological experiments using single cells as anchoring points (e.g., 1 cell vs. 1000 cells per “tube”), achieving higher resolution and potentially more relevant data for modeling and downstream analyses. We demonstrate the ability of PULSE to perform biofabrication, precision gating, and deterministic array barcoding via preallocated droplet-addressable primers. Single cells can be gently printed at a speed range of 5–20 cell⋅s−1 with an accuracy of 90.5–97.7%, which can then adhere to the substrate and grow for up to 72 h while preserving cell integrity. In the deterministic barcoding experiment, 95.6% barcoding accuracy and 2.7% barcode hopping were observed by comparing the phenotypic data with known genotypic data from two types of single cells. Our PULSE platform allows for precise and dynamic analyses by automating experiments at the single-cell level, offering researchers a powerful tool in biomedical research.
Measurable residual disease testing and allogeneic hematopoietic cell transplantation for AML: adapting Pre-MEASURE to clinical practice
Authors: Shaffer Brian C. , Kebriaei Partow , de Lima Marcos , Jimenez Jimenez Antonio M. 
Published: November 2024

Abstract
Measurable residual disease (MRD) testing in patients with acute myelogenous leukemia (AML) represents a heterogenous assessment process designed to quantify leukemia-specific biomarkers that are not ascertainable by routine pathologic evaluation. The most common tools used to assess MRD are multiparameter flow cytometry (MPFC), and polymerase chain reaction (PCR) based tools, including quantitative or digital droplet PCR (qPCR, ddPCR), or next-generation sequencing (NGS) technologies. Collectively, MRD assessments have become an important clinical tool in the management of patients with AML. Despite progress, significant questions remain with respect to the appropriate timing, frequency, and methodology of MRD assessment, and whether or how to adapt therapy based on MRD results. Recent data from the Pre-MEASURE study, a retrospective cohort analysis of error corrected NGS based MRD assessment prior to allogeneic hematopoietic cell transplantation (alloHCT) in patients with AML, provides additional key information with respect to the emerging role of NGS-based technology in MRD assessment. In the context of this review, we evaluate the Pre-MEASURE study as well as other recent, high-quality assessments of MRD in AML. Our focus is to provide a practical assessment of the use of emerging MRD technologies in patients with AML with an emphasis on the role of peri-transplant MRD for the practicing clinician.
Engineering bone/cartilage organoids: strategy, progress, and application
Authors: Bai Long , Zhou Dongyang , Li Guangfeng , Liu Jinlong , Chen Xiao , Su Jiacan 
Published: November 2024

AbstractThe concept and development of bone/cartilage organoids are rapidly gaining momentum, providing opportunities for both fundamental and translational research in bone biology. Bone/cartilage organoids, essentially miniature bone/cartilage tissues grown in vitro, enable the study of complex cellular interactions, biological processes, and disease pathology in a representative and controlled environment. This review provides a comprehensive and up-to-date overview of the field, focusing on the strategies for bone/cartilage organoid construction strategies, progresses in the research, and potential applications. We delve into the significance of selecting appropriate cells, matrix gels, cytokines/inducers, and construction techniques. Moreover, we explore the role of bone/cartilage organoids in advancing our understanding of bone/cartilage reconstruction, disease modeling, drug screening, disease prevention, and treatment strategies. While acknowledging the potential of these organoids, we discuss the inherent challenges and limitations in the field and propose potential solutions, including the use of bioprinting for organoid induction, AI for improved screening processes, and the exploration of assembloids for more complex, multicellular bone/cartilage organoids models. We believe that with continuous refinement and standardization, bone/cartilage organoids can profoundly impact patient-specific therapeutic interventions and lead the way in regenerative medicine.
Androgen-targeted hsa_circ_0085121 encodes a novel protein and improves the development of prostate cancer through facilitating the activity of PI3K/Akt/mTOR pathway and enhancing AR-V7 alternative splicing
Authors: Li Jianfeng , Qiu Hui , Dong Qingzhuo , Yu Hongyuan , Piao Chiyuan , Li Zhengxiu , Sun Yanbin , Cui Xiaolu 
Published: November 2024

AbstractProstate cancer (PCa) is the most prevalent type of cancer and the second leading cause of mortality in males, with a marked increase in incidence observed across the globe. In the present study, whole-transcriptome analysis was conducted to identify differentially expressed circular RNAs (DE-circRNAs). The coding abilities of the DE-circRNAs were analyses, and it was found that hsa_circ_0085121 (circRNF19A) not only exhibited overexpression in PCa cells and tumor samples, but also encoded a 490 amino acid polypeptide designated circRNF19A-490aa. The knockdown of circRNF19A was observed to notably inhibit the proliferation, invasion, migration and docetaxel resistance of PCa cells. In contrast, mutation of the IRES significantly impaired the tumor-promoting function of circRNF19A, indicating that circRNF19A-490aa is the primary form that regulates the malignant behaviors of PCa cells. Mechanistically, circRNF19A-490aa was demonstrated to interact with HSP90AA1, thereby enhancing AR activity and facilitating the activation of the Akt/mTOR and PLK1 pathways. Furthermore, circRNF19A-490aa was observed to interact with HNRNPF, facilitating the recruitment of HNRNPF to the splicing site of AR-V7 and enhancing its alternative splicing. Finally, the androgen receptor (AR) was observed to bind to the promoter region of the RNF19A gene, subsequently regulating the expression of circRNF19A and circRNF19A-490aa. These data indicate that circRNF19A plays a pivotal role in AR activation and AR-V7 generation by encoding a novel protein, circRNF19A-490aa, and targeting circRNF19A may prove an effective strategy for impeding the progression of CRPC.
Arginine methylation-dependent TRIM47 stability mediated by CARM1 promotes the metastasis of hepatocellular carcinoma
Authors: Tang Yuzhe , Meng Xiang , Luo Xia , Yao Wentao , Tian Li , Zhang Zijian , Zhao Yuan , Xiao Juan , Zhu Haichuan , Hu Jia 
Published: November 2024

AbstractThe tripartite motif (TRIM) protein family has been shown to play important roles in the occurrence and development of various tumors. However, the biological functions of TRIM47 and its regulatory mechanism in hepatocellular carcinoma (HCC) remain unexplored. Here, we showed that TRIM47 was upregulated in HCC tissues compared with adjacent normal tissues, especially at advanced stages, and associated with poor prognosis in HCC patients. Functional studies demonstrated that TRIM47 enhanced the migration and invasion ability of HCC cells in vitro and in vivo. Mechanistically, TRIM47 promotes HCC metastasis through interacting with SNAI1 and inhibiting its degradation by proteasome. Moreover, TRIM47 was di-methylated by CARM1 at its arginine 210 (R210) and arginine 582 (R582), which protected TRIM47 from the ubiquitination and degradation mediated by E3 ubiquitin ligase complex CRL4CRBN. Collectively, our study reveals a pro-metastasis role of TRIM47 in HCC, unveils a unique mechanism controlling TRIM47 stability by CARM1 mediated arginine methylation, and highlights the role of the CARM1-CRL4CRBN-TRIM47-SNAI1 axis in HCC metastasis. This work may provide potential therapeutic targets for metastatic HCC treatment.
Unveiling RNA structure-mediated regulations of RNA stability in wheat
Authors: Wu Haidan , Yu Haopeng , Zhang Yueying , Yang Bibo , Sun Wenqing , Ren Lanying , Li Yuchen , Li Qianqian , Liu Bao , Ding Yiliang , Zhang Huakun 
Published: November 2024

AbstractDespite the critical role of mRNA stability in post-transcriptional gene regulation, research on this topic in wheat, a vital agricultural crop, remains unclear. Our study investigated the mRNA decay landscape of durum wheat (Triticum turgidum L. ssp. durum, BBAA), revealing subgenomic asymmetry in mRNA stability and its impact on steady-state mRNA abundance. Our findings indicate that the 3’ UTR structure and homoeolog preference for RNA structural motifs can influence mRNA stability, leading to subgenomic RNA decay imbalance. Furthermore, single-nucleotide variations (SNVs) selected for RNA structural motifs during domestication can cause variations in subgenomic mRNA stability and subsequent changes in steady-state expression levels. Our research on the transcriptome stability of polyploid wheat highlights the regulatory role of non-coding region structures in mRNA stability, and how domestication shaped RNA structure, altering subgenomic mRNA stability. These results illustrate the importance of RNA structure-mediated post-transcriptional gene regulation in wheat and pave the way for its potential use in crop improvement.
Microbial and mineral interactions decouple litter quality from soil organic matter formation
Authors: Elias Dafydd M. O. , Mason Kelly E. , Goodall Tim , Taylor Ashley , Zhao Pengzhi , Otero-Fariña Alba , Chen Hongmei , Peacock Caroline L. , Ostle Nicholas J. , Griffiths Robert , Chapman Pippa J. , Holden Joseph , Banwart Steve , McNamara Niall P. , Whitaker Jeanette 
Published: November 2024

AbstractCurrent understanding of soil carbon dynamics suggests that plant litter quality and soil mineralogy control the formation of mineral-associated soil organic carbon (SOC). Due to more efficient microbial anabolism, high-quality litter may produce more microbial residues for stabilisation on mineral surfaces. To test these fundamental concepts, we manipulate soil mineralogy using pristine minerals, characterise microbial communities and use stable isotopes to measure decomposition of low- and high-quality litter and mineral stabilisation of litter-C. We find that high-quality litter leads to less (not more) efficient formation of mineral-associated SOC due to soil microbial community shifts which lower carbon use efficiency. Low-quality litter enhances loss of pre-existing SOC resulting in no effect of litter quality on total mineral-associated SOC. However, mineral-associated SOC formation is primarily controlled by soil mineralogy. These findings refute the hypothesis that high-quality plant litters form mineral-associated SOC most efficiently and advance our understanding of how mineralogy and litter-microbial interactions regulate SOC formation.
Arctic freshwater anomaly transiting to the North Atlantic delayed within a buffer zone
Authors: Wang Qiang , Danilov Sergey , Jung Thomas 
Published: November 2024

AbstractA two-decade-long accumulation of freshwater in the Arctic Ocean’s Beaufort Gyre has recently started to be released. Here we use satellite observations and model simulations to show that changes in wind regimes and sea ice declines are causing freshwater to accumulate close to the export gateways to the North Atlantic. This emerging buffer zone plays an important role in modulating the propagation of freshwater into the subpolar North Atlantic.
Single-cell integration reveals metaplasia in inflammatory gut diseases
Authors: Oliver Amanda J. , Huang Ni , Bartolome-Casado Raquel , Li Ruoyan , Koplev Simon , Nilsen Hogne R. , Moy Madelyn , Cakir Batuhan , Polanski Krzysztof , Gudiño Victoria , Melón-Ardanaz Elisa , Sumanaweera Dinithi , Dimitrov Daniel , Milchsack Lisa Marie , FitzPatrick Michael E. B. , Provine Nicholas M. , Boccacino Jacqueline M. , Dann Emma , Predeus Alexander V. , To Ken , Prete Martin , Chapman Jonathan A. , Masi Andrea C. , Stephenson Emily , Engelbert Justin , Lobentanzer Sebastian , Perera Shani , Richardson Laura , Kapuge Rakeshlal , Wilbrey-Clark Anna , Semprich Claudia I. , Ellams Sophie , Tudor Catherine , Joseph Philomeena , Garrido-Trigo Alba , Corraliza Ana M. , Oliver Thomas R. W. , Hook C. Elizabeth , James Kylie R. , Mahbubani Krishnaa T. , Saeb-Parsy Kourosh , Zilbauer Matthias , Saez-Rodriguez Julio , Høivik Marte Lie , Bækkevold Espen S. , Stewart Christopher J. , Berrington Janet E. , Meyer Kerstin B. , Klenerman Paul , Salas Azucena , Haniffa Muzlifah , Jahnsen Frode L. , Elmentaite Rasa , Teichmann Sarah A. 
Published: November 2024

AbstractThe gastrointestinal tract is a multi-organ system crucial for efficient nutrient uptake and barrier immunity. Advances in genomics and a surge in gastrointestinal diseases1,2 has fuelled efforts to catalogue cells constituting gastrointestinal tissues in health and disease3. Here we present systematic integration of 25 single-cell RNA sequencing datasets spanning the entire healthy gastrointestinal tract in development and in adulthood. We uniformly processed 385 samples from 189 healthy controls using a newly developed automated quality control approach (scAutoQC), leading to a healthy reference atlas with approximately 1.1 million cells and 136 fine-grained cell states. We anchor 12 gastrointestinal disease datasets spanning gastrointestinal cancers, coeliac disease, ulcerative colitis and Crohn’s disease to this reference. Utilizing this 1.6 million cell resource (gutcellatlas.org), we discover epithelial cell metaplasia originating from stem cells in intestinal inflammatory diseases with transcriptional similarity to cells found in pyloric and Brunner’s glands. Although previously linked to mucosal healing4, we now implicate pyloric gland metaplastic cells in inflammation through recruitment of immune cells including T cells and neutrophils. Overall, we describe inflammation-induced changes in stem cells that alter mucosal tissue architecture and promote further inflammation, a concept applicable to other tissues and diseases.
A spatial human thymus cell atlas mapped to a continuous tissue axis
Authors: Yayon Nadav , Kedlian Veronika R. , Boehme Lena , Suo Chenqu , Wachter Brianna T. , Beuschel Rebecca T. , Amsalem Oren , Polanski Krzysztof , Koplev Simon , Tuck Elizabeth , Dann Emma , Van Hulle Jolien , Perera Shani , Putteman Tom , Predeus Alexander V. , Dabrowska Monika , Richardson Laura , Tudor Catherine , Kreins Alexandra Y. , Engelbert Justin , Stephenson Emily , Kleshchevnikov Vitalii , De Rita Fabrizio , Crossland David , Bosticardo Marita , Pala Francesca , Prigmore Elena , Chipampe Nana-Jane , Prete Martin , Fei Lijiang , To Ken , Barker Roger A. , He Xiaoling , Van Nieuwerburgh Filip , Bayraktar Omer Ali , Patel Minal , Davies E Graham , Haniffa Muzlifah A. , Uhlmann Virginie , Notarangelo Luigi D. , Germain Ronald N. , Radtke Andrea J. , Marioni John C. , Taghon Tom , Teichmann Sarah A. 
Published: November 2024

AbstractT cells develop from circulating precursor cells, which enter the thymus and migrate through specialized subcompartments that support their maturation and selection1. In humans, this process starts in early fetal development and is highly active until thymic involution in adolescence. To map the microanatomical underpinnings of this process in pre- and early postnatal stages, we established a quantitative morphological framework for the thymus—the Cortico-Medullary Axis—and used it to perform a spatially resolved analysis. Here, by applying this framework to a curated multimodal single-cell atlas, spatial transcriptomics and high-resolution multiplex imaging data, we demonstrate establishment of the lobular cytokine network, canonical thymocyte trajectories and thymic epithelial cell distributions by the beginning of the the second trimester of fetal development. We pinpoint tissue niches of thymic epithelial cell progenitors and distinct subtypes associated with Hassall’s corpuscles and identify divergence in the timing of medullary entry between CD4 and CD8 T cell lineages. These findings provide a basis for a detailed understanding of T lymphocyte development and are complemented with a holistic toolkit for cross-platform imaging data analysis, annotation and OrganAxis construction (TissueTag), which can be applied to any tissue.
A multi-omic atlas of human embryonic skeletal development
Authors: To Ken , Fei Lijiang , Pett J. Patrick , Roberts Kenny , Blain Raphael , Polański Krzysztof , Li Tong , Yayon Nadav , He Peng , Xu Chuan , Cranley James , Moy Madelyn , Li Ruoyan , Kanemaru Kazumasa , Huang Ni , Megas Stathis , Richardson Laura , Kapuge Rakesh , Perera Shani , Tuck Elizabeth , Wilbrey-Clark Anna , Mulas Ilaria , Memi Fani , Cakir Batuhan , Predeus Alexander V. , Horsfall David , Murray Simon , Prete Martin , Mazin Pavel , He Xiaoling , Meyer Kerstin B. , Haniffa Muzlifah , Barker Roger A. , Bayraktar Omer , Chédotal Alain , Buckley Christopher D. , Teichmann Sarah A. 
Published: November 2024

AbstractHuman embryonic bone and joint formation is determined by coordinated differentiation of progenitors in the nascent skeleton. The cell states, epigenetic processes and key regulatory factors that underlie lineage commitment of these cells remain elusive. Here we applied paired transcriptional and epigenetic profiling of approximately 336,000 nucleus droplets and spatial transcriptomics to establish a multi-omic atlas of human embryonic joint and cranium development between 5 and 11 weeks after conception. Using combined modelling of transcriptional and epigenetic data, we characterized regionally distinct limb and cranial osteoprogenitor trajectories across the embryonic skeleton and further described regulatory networks that govern intramembranous and endochondral ossification. Spatial localization of cell clusters in our in situ sequencing data using a new tool, ISS-Patcher, revealed mechanisms of progenitor zonation during bone and joint formation. Through trajectory analysis, we predicted potential non-canonical cellular origins for human chondrocytes from Schwann cells. We also introduce SNP2Cell, a tool to link cell-type-specific regulatory networks to polygenic traits such as osteoarthritis. Using osteolineage trajectories characterized here, we simulated in silico perturbations of genes that cause monogenic craniosynostosis and implicate potential cell states and disease mechanisms. This work forms a detailed and dynamic regulatory atlas of bone and cartilage maturation and advances our fundamental understanding of cell-fate determination in human skeletal development.