bluuebunny/crossref_metadata_2025_split huggingface dataset:
HemaScope: A Tool for Analyzing Single-cell and Spatial Transcriptomics Data of Hematopoietic Cells
Authors: Wang Zhenyi , Miao Yuxin , Li Hongjun , Cheng Wenyan , Shi Minglei , Gang Lv , Zhu Yating , Zhang Junyi , Tan Tingting , Gu Jin , Zhang Michael Q , Li Jianfeng , Fang Hai , Chen Zhu , Chen Saijuan 
Published: January 2025

Abstract
Single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics (ST) techniques hold great value in evaluating the heterogeneity and spatial characteristics of hematopoietic cells within tissues. These two techniques are highly complementary, with scRNA-seq offering single-cell resolution and ST retaining spatial information. However, there is an urgent demand for well-organized and user-friendly toolkits capable of handling single-cell and spatial information. Here, we present HemaScope, a specialized bioinformatics toolkit featuring modular designs to analyze scRNA-seq and ST data generated from hematopoietic cells. It enables users to perform quality control, basic analysis, cell atlas construction, cellular heterogeneity exploration, and dynamical examination on scRNA-seq data. Also, it can perform spatial analysis and microenvironment analysis on ST data. Meanwhile, HemaScope takes into consideration hematopoietic cell-specific features, including lineage affiliation evaluation, cell cycle prediction, and marker gene collection. To enhance the user experience, we have deployed the toolkit in user-friendly forms: HemaScopeR (an R package), HemaScopeCloud (a web server), HemaScopeDocker (a Docker image), and HemaScopeShiny (a graphical interface). In case studies, we employed it to construct a cell atlas of human bone marrow, analyze age-related changes, and identify acute myeloid leukemia cells in mice. Moreover, we characterized the microenvironments in angioimmunoblastic T cell lymphoma and primary central nervous system lymphoma, elucidating tumor boundaries. HemaScope is freely available at https://zhenyiwangthu.github.io/HemaScope_Tutorial/.
The cop and the mob: Joe Petrosino against the Mafia in the United States and Italy during the Progressive Era
Authors: Landolfi Francesco 
Published: January 2025

Abstract
This article reconstructs the clash between local police and Italian crime in New York during the Progressive Era. During the 1900s the Black Hand organized crime began to blackmail Italian businesses and, to counter this felony, the New York Police Department decided to establish Detective Joseph Petrosino’s Italian Squad. The clash between Petrosino and the Black Hand lasted until 1909, when the officer was killed in Palermo. However, the death of the Italian American detective led to the conviction of the alleged contract murderers and, finally, to the end of the Black Hand in the early 1910s.
High ectomycorrhizal relative abundance during winter at the treeline
Authors: Saona Luis A , Oporto Christian I , Villarreal Pablo , Urbina Kamila , Correa Cristian , Quintero-Galvis Julian F , Moreno-Meynard Paulo , Piper Frida I , Vianna Juliana A , Nespolo Roberto F , Cubillos Francisco A 
Published: January 2025

Abstract
The rhizosphere is the soil region around plant roots hosting a diverse microbial community, influencing nutrient availability and how plants react to extreme conditions. However, our understanding of the fungi biodiversity and the impact of environmental variations on this biodiversity is still in its infancy. Our study investigates fungal communities’ diversity and functional traits in the rhizosphere of Nothofagus pumilio, one of the few winters deciduous treeline species in the world, forming the treeline in southern South America. At four distinct locations covering 10° latitude, we collected soil samples at treeline and 200 m below over four seasons during a single year. We employed ITS metabarcoding to elucidate fungal community structures. Our results reveal that fungal diversity was mainly determined by latitudinal variation, with higher levels during warmer seasons and lower altitudes. Interestingly, we found a marked dominance of ectomycorrhizal fungi at the treeline, particularly during the winter. In contrast, saprotrophic fungi were more abundant at lower altitudes, particularly during the warmer spring and summer seasons. These findings highlight the temporal and spatial dynamics of rhizospheric fungal communities and their potential roles in ecological processes, emphasizing the value of these communities as indicators of environmental change in high-elevation forests.
AXpert: human expert facilitated privacy-preserving large language models for abdominal X-ray report labeling
Authors: Zhang Yufeng , Kohne Joseph G , Webster Katherine , Vartanian Rebecca , Wittrup Emily , Najarian Kayvan 
Published: January 2025

Abstract

Importance
The lack of a publicly accessible abdominal X-ray (AXR) dataset has hindered necrotizing enterocolitis (NEC) research. While significant strides have been made in applying natural language processing (NLP) to radiology reports, most efforts have focused on chest radiology. Development of an accurate NLP model to identify features of NEC on abdominal radiograph can support efforts to improve diagnostic accuracy for this and other rare pediatric conditions.

Objectives
This study aims to develop privacy-preserving large language models (LLMs) and their distilled version to efficiently annotate pediatric AXR reports.

Materials and Methods
Utilizing pediatric AXR reports collected from C.S. Mott Children’s Hospital, we introduced AXpert in 2 formats: one based on the instruction-fine-tuned 7-B Gemma model, and a distilled version employing a BERT-based model derived from the fine-tuned model to improve inference and fine-tuning efficiency. AXpert aims to detect NEC presence and classify its subtypes—pneumatosis, portal venous gas, and free air.

Results
Extensive testing shows that LLMs, including Axpert, outperforms baseline BERT models on all metrics. Specifically, Gemma-7B (F1 score: 0.9 ± 0.015) improves upon BlueBERT by 132% in F1 score for detecting NEC positive samples. The distilled BERT model matches the performance of the LLM labelers and surpasses expert-trained baseline BERT models.

Discussion
Our findings highlight the potential of using LLMs for clinical NLP tasks. With minimal expert knowledge injections, LLMs can achieve human-like performance, greatly reducing manual labor. Privacy concerns are alleviated as all models are trained and deployed locally.

Conclusion
AXpert demonstrates potential to reduce human labeling efforts while maintaining high accuracy in automating NEC diagnosis with AXR, offering precise image labeling capabilities.
Probability of achieving bone mineral density treatment goals with denosumab treatment in postmenopausal women with osteoporosis
Authors: Cosman Felicia , Wang Zhenxun , Li Xiaodong , Cummings Steven R 
Published: January 2025

Abstract
BMD levels achieved on osteoporosis treatment are predictive of subsequent fracture risk, and T-score &gt;−2.5 has been proposed as a minimum treatment target for women with osteoporosis. Knowing the likelihood of attaining target T-scores with different medications for different baseline BMD levels can help determine appropriate initial treatment for individual patients. In this post hoc analysis, we estimated the probability of achieving a non-osteoporotic T-score (&gt;−2.5 or ≥−2.0) at the TH or LS in postmenopausal women &gt;60 yr old treated with denosumab for either 3 or 10 yr in the FREEDOM trial and its long-term extension. In women with baseline TH T-scores of −2.7, −3.0, and −3.5, the probabilities of achieving target T-scores &gt;−2.5 with 3 yr of denosumab were 71%, 12%, and 0.1%, respectively. At LS, for baseline T-scores of −2.7, −3.0, and −3.5, the probabilities were 86%, 59%, and 11%, respectively. Longer treatment duration of up to 10 yr increased the probability of achieving target T-scores. The baseline T-scores that permitted at least 50% of women to achieve a target T-score &gt;−2.5 were −2.8 at TH and −3.1 at LS after 3 yr and −3.0 at TH and −3.7 at LS after 10 yr of treatment. To achieve higher treatment targets (T-scores ≥ −2.0), overall probabilities were lower at both skeletal sites, particularly for TH, even with longer treatment duration. Our results demonstrate that the probability of achieving T-score targets with denosumab is dependent on baseline BMD, skeletal site, and treatment duration. Knowing the probability of achieving treatment targets for different baseline TH and LS T-scores can help determine whether denosumab is an appropriate first choice of treatment in individual patients.
Epiregulin ameliorates ovariectomy-induced bone loss through orchestrating the differentiation of osteoblasts and osteoclasts
Authors: Dong Yuan , Wu Xiaowen , Hao Yinglong , Liu Wei , Hu Xingli , Zhou Jie , Li Xiaoxia , Wang Baoli 
Published: January 2025

Abstract
Epiregulin plays a role in a range of biological activities including malignancies. This study aims to investigate the potential contribution of epiregulin to bone cell differentiation and bone homeostasis. The data showed that epiregulin expression was upregulated during osteogenesis but downregulated during adipogenesis. Functionally, epiregulin promoted osteoblast differentiation while inhibiting adipocyte differentiation from mesenchymal progenitor cells. Epidermal growth factor receptor (EGFR), one of the two known receptors for epiregulin, exerted opposing effects compared to epiregulin. Intriguingly, silencing EGFR almost completely abolished the dysregulation of osteoblast and adipocyte differentiation induced by epiregulin, suggesting that EGFR is indispensable for mediating epiregulin function. Further mechanistic exploration indicated that epiregulin/EGFR signaled via the inactivation of mechanistic target of rapamycin complex 1 (mTORC1) pathway. Moreover, epiregulin downregulated receptor activator of nuclear factor-κB ligand (RANKL) expression in BMSCs and inhibited the differentiation of bone marrow osteoclast precursor cells into osteoclasts. Treatment of ovariectomized female mice with recombinant epiregulin increased osteoblasts and bone formation, decreased osteoclasts and bone resorption, and ameliorated cancellous bone loss. Consistently, epiregulin treatment improved the potential of BMSCs to differentiate into osteoblasts. Collectively, this study has identified a critical role of epiregulin in regulating osteoblast differentiation through EGFR-mediated inactivation of mTORC1 pathway, as well as osteoclast differentiation via a mechanism associated with RANKL signaling. Additionally, it highlights the potential of epiregulin as a strategy for combating osteoporosis.
Measuring the effect of RFID and marker recognition tags on cockroach (Blattodea: Blaberidae) behavior using AI-aided tracking
Authors: McLean Callum J , Fisher David N 
Published: January 2025

Abstract
Radio frequency identification (RFID) technology and marker recognition algorithms can offer an efficient and non-intrusive means of tracking animal positions. As such, they have become important tools for invertebrate behavioral research. Both approaches require fixing a tag or marker to the study organism, and so it is useful to quantify the effects such procedures have on behavior before proceeding with further research. However, frequently studies do not report doing such tests. Here, we demonstrate a time-efficient and accessible method for quantifying the impact of tagging on individual movement using open-source automated video tracking software. We tested the effect of RFID tags and tags suitable for marker recognition algorithms on the movement of Argentinian wood roaches (Blapicta dubia, Blattodea: Blaberidae) by filming tagged and untagged roaches in laboratory conditions. We employed DeepLabCut on the resultant videos to track cockroach movement and extract measures of behavioral traits. We found no statistically significant differences between RFID tagged and untagged groups in average speed over the trial period, the number of unique zones explored, and the number of discrete walks. However, groups that were tagged with labels for marker recognition had significantly higher values for all 3 metrics. We therefore support the use of RFID tags to monitor the behavior of B. dubia but note that the effect of using labels suitable for label recognition to identify individuals should be taken into consideration when measuring B.dubia behavior. We hope that this study can provide an accessible and viable roadmap for further work investigating the effects of tagging on insect behavior.
Feeling out-of-sync: navigating new rhythms in places of settlement
Authors: Kale Amber , Kindon Sara , Stupples Polly 
Published: January 2025

Abstract
In this article, we draw upon Lefebvre’s method of rhythmanalysis to analyse themes emerging from a participatory research project with former refugees in Aotearoa New Zealand. Specifically, we explore how participants navigate everyday rhythms, routines, and cycles in new places, and the nuanced ways in which these repetitive time structures influence their sense of place attachment and well-being. While resettlement discourse prioritizes abstract, linear framings of time, our research suggested that concrete temporal experiences (such as the pace-of-life and changing seasonal cycles) are also important to consider. Being out-of-sync with everyday rhythms evoked disorientation and discomfort for participants, while synchronizing and/or syncopating with local rhythms helped them to maintain important habits and routines and regain a sense of stability. We therefore argue for a broader conceptualization of time in resettlement, which considers how everyday rhythms are embodied and felt by former refugees in ways that influence their well-being and wider resettlement outcomes.
A lipoxygenase gene modulates jasmonate biosynthesis to enhance blast resistance in rice
Authors: Wang Lanlan , Chen Yumeng , Deng Fan , Jin Gaochen , Gong Xue , Wu Gengwei , Zhang Chi , Li Ran , Wang Hua 
Published: January 2025

Abstract
Inhibition of jasmonic acid (JA) signaling renders plants more susceptible to biotic stresses. Pathogen infection can induce an increase in JA levels. However, our understanding of the mechanisms mediating pathogen-induced JA accumulation in rice (Oryza sativa) remains limited. We characterized OsLOX9, a lipoxygenase gene of the 13-LOX subfamily involved in JA biosynthesis, which is induced upon infection by the rice blast fungus Magnaporthe oryzae. Two independent lox9 mutants exhibited increased susceptibility to M. oryzae infection, a phenotype that was fully restored by methyl jasmonate treatment, and showed reduced pathogen-induced accumulation of 12-oxo-phytodienoic acid, JA, and its bioactive form JA-Ile. RNA sequencing-based expression analysis in response to M. oryzae infection revealed an essential role of OsLOX9-produced jasmonates in up-regulating terpenoid phytoalexin pathway genes. Furthermore, we found that the JA core transcription factor, OsMYC2, can bind to the promoter of OsLOX9 and activate its expression, creating a positive feedback loop during pathogenesis. This study reveals that OsLOX9 is a key blast fungus-induced JA biosynthesis gene and contributes to resistance to blast disease in rice.
The AIRI plug-and-play algorithm for image reconstruction in radio-interferometry: variations and robustness
Authors: Terris Matthieu , Tang Chao , Jackson Adrian , Wiaux Yves 
Published: January 2025

ABSTRACT
Plug-and-play (PnP) algorithms are appealing alternatives to proximal algorithms when solving inverse imaging problems. By learning a Deep Neural Network (DNN) denoiser behaving as a proximal operator, one waives the computational complexity of optimization algorithms induced by sophisticated image priors, and the sub-optimality of handcrafted priors compared to DNNs. Such features are highly desirable in radio-interferometric (RI) imaging, where precision and scalability of the image reconstruction process are key. In previous work, we introduced AIRI (‘AI Regularization in radio-interferometric Imaging’), PnP counterpart to the unconstrained variant of the SARA (Sparsity Averaging Reweighted Analysis) optimization algorithm, relying on a forward–backward algorithmic backbone. Here, we introduce variations of AIRI towards a more general and robust PnP paradigm in RI imaging. First, we show that the AIRI denoisers can be used without any alteration to instantiate a PnP counterpart to the constrained SARA optimization algorithm itself, relying on a primal-dual forward–backward algorithmic backbone, thus extending the remit of the AIRI paradigm. Secondly, we show that AIRI algorithms are robust to strong variations in the nature of the training data set, with denoisers trained on medical images yielding similar reconstruction quality to those trained on astronomical images. Thirdly, we develop a functionality to quantify the model uncertainty introduced by the randomness in the training process. We validate the image reconstruction and uncertainty quantification functionality of AIRI algorithms against the SARA family and CLEAN, both in simulation and on real data of the ESO 137-006 galaxy acquired with the MeerKAT telescope. AIRI code is available in the BASPLib code library$^\dagger$ on GitHub.
The Gefion Asteroid Family: parent body puzzles and ordinary chondrite pieces
Authors: McGraw Allison , Reddy Vishnu , Sanchez Juan A 
Published: January 2025

ABSTRACT
Asteroid families provide critical clues to the nature of their original parent bodies. Ordinary chondrites, the most common meteorites to reach Earth, consist of three subtypes: H, L, and LL chondrites, offering valuable insights into the Solar system’s geochemical history. The Gefion Asteroid Family (GAF) has been proposed as a source for some L chondrites. In this study, we present the results of a spectroscopic campaign on dynamically defined members of the GAF, testing the hypothesis that L chondrites may originate from this family. Our new observations, combined with near-infrared (NIR) spectra from previous work, provide data for 18 asteroids. Compositional analysis reveals a range of meteorite analogues, including H (1 object, 6 per cent), L (8 objects, 43 per cent), and LL (1 object, 6 per cent). Objects with L chondrite-like compositions were the most common in our sample. Accounting for uncertainties, we also observed intermediate subtypes, such as H/L (5 objects, 28 per cent) and L/LL (3 objects, 17 per cent). Based on these results, we conclude that the GAF is a viable source for some L chondrite meteorites. However, further investigations are needed to fully understand the family’s contribution to the broader meteorite population.
Protest Chants as Public Music Theory
Authors: Manabe Noriko 
Published: January 2025

Abstract
This article recounts a music theorist’s experience with transcribing and analyzing protest chants as a form of public music theory, drawing from over a decade of fieldwork at demonstrations in Japan and the United States, including antinuclear protests in Japan, the Women’s March, Black Lives Matter demonstrations, and protests related to reproductive freedom and gun control. While exploring how music analysis can serve public needs, the project also raises important methodological and ethical questions. The transcriptions demonstrate how protesters use rhythmic patterns, intonation, and musical structures to build solidarity and amplify their message, often drawing on historical precedents and popular culture. By publishing analyses through open-access platforms and social media, I make musical transcriptions and insights available to activists and the public. However, this approach also reveals tensions between academic and public-facing scholarship, including questions about notation methods, the limitations of transcription, recognition of the work as scholarship by colleagues, and the role of social media in knowledge dissemination. The article ultimately considers how music theorists can meaningfully engage with contemporary social movements while navigating the challenges of public scholarship in a digital age.
c-JUN: a chromatin repressor that limits mesoderm differentiation in human pluripotent stem cells
Authors: Zhang Ran , Li Guihuan , Zhang Qi , Wang Zhenhua , Xiang Dan , Zhang Xiaofei , Chen Jiekai , Hutchins Andrew P , Qin Dajiang , Su Huanxing , Pei Duanqing , Li Dongwei 
Published: January 2025

Abstract
Cell fate determination at the chromatin level is not fully comprehended. Here, we report that c-JUN acts on chromatin loci to limit mesoderm cell fate specification as cells exit pluripotency. Although c-JUN is widely expressed across various cell types in early embryogenesis, it is not essential for maintaining pluripotency. Instead, it functions as a repressor to constrain mesoderm development while having a negligible impact on ectoderm differentiation. c-JUN interacts with MBD3–NuRD complex, which helps maintain chromatin in a low accessibility state at mesoderm-related genes during the differentiation of human pluripotent stem cells into mesoderm. Furthermore, c-JUN specifically inhibits the activation of key mesoderm factors, such as EOMES and GATA4. Knocking out c-JUN or inhibiting it with a JNK inhibitor can alleviate this suppression, promoting mesoderm cell differentiation. Consistently, knockdown of MBD3 enhances mesoderm generation, whereas MBD3 overexpression impedes it. Overexpressing c-JUN redirects differentiation toward a fibroblast-like lineage. Collectively, our findings suggest that c-JUN acts as a chromatin regulator to restrict the mesoderm cell fate.
Genomic clustering tendency of transcription factors reflects phase-separated transcriptional condensates at super-enhancers
Authors: Wang Shengyuan , Wang Zhenjia , Zang Chongzhi 
Published: January 2025

Abstract
Many transcription factors (TFs) have been shown to bind to super-enhancers, forming transcriptional condensates to activate transcription in various cellular systems. However, the genomic and epigenomic determinants of phase-separated transcriptional condensate formation remain poorly understood. Questions regarding which TFs tend to associate with transcriptional condensates and what factors influence their association are largely unanswered. Here we systematically analyzed 571 DNA sequence motifs across the human genome and 6650 TF binding profiles across different cell types to identify the molecular features contributing to the formation of transcriptional condensates. We found that the genomic distributions of sequence motifs for different TFs exhibit distinct clustering tendencies. Notably, TF motifs with a high genomic clustering tendency are significantly associated with super-enhancers. TF binding profiles showing a high genomic clustering tendency are further enriched at cell-type-specific super-enhancers. TFs with a high binding clustering tendency also possess high liquid–liquid phase separation abilities. Compared to nonclustered TF binding, densely clustered TF binding sites are more enriched at cell-type-specific super-enhancers with higher chromatin accessibility, elevated chromatin interaction and stronger association with cancer outcomes. Our results indicate that the clustered genomic binding patterns and the phase separation properties of TFs collectively contribute to the formation of transcriptional condensates.