bluuebunny/crossref_metadata_2025_split huggingface dataset:
Chemical perturbations impacting histone acetylation govern colorectal cancer differentiation
Authors: Likasitwatanakul Pornlada , Li Zhixin , Doan Paul , Spisak Sandor , Raghawan Akhouri Kishore , Liu Qi , Liow Priscilla , Lee Sunwoo , Chen David , Bala Pratyusha , Sahgal Pranshu , Aitymbayev Daulet , Thalappillil Jennifer S. , Papanastasiou Malvina , Hawkins William , Carr Steven A. , Park Haeseong , Cleary James M. , Qi Jun , Sethi Nilay S. 
Published: December 2024

ABSTRACTDysregulated epigenetic programs that restrict differentiation, reactivate fetal genes, and confer phenotypic plasticity are critical to colorectal cancer (CRC) development. By screening a small molecule library targeting epigenetic regulators using our dual reporter system, we found that inhibiting histone deacetylase (HDAC) 1/2 promotes CRC differentiation and anti-tumor activity. Comprehensive biochemical, chemical, and genetic experiments revealed that on-target blockade of the HDAC1/2 catalytic domain mediated the differentiated phenotype. Unbiased profiling of histone posttranslational modifications induced by HDAC1/2 inhibition nominated acetylation of specific histone lysine residues as potential regulators of differentiation. Genome-wide assessment of implicated marks indicated that H3K27ac gains at HDAC1/2-bound regions associated with open chromatin and upregulation of differentiation genes upon HDAC1/2 inhibition. Disrupting H3K27ac by degrading acetyltransferase EP300 rescued HDAC1/2 inhibitor-mediated differentiation of a patient-derived CRC model using single cell RNA-sequencing. Genetic screens revealed that DAPK3 contributes to CRC differentiation induced by HDAC1/2 inhibition. These results highlight the importance of specific chemically targetable histone modifications in governing cancer cell states and epigenetic reprogramming as a therapeutic strategy in CRC.BRIEF SUMMARYHDAC1/2 inhibition promotes colorectal cancer differentiation via gains in H3K27ac, which can be reversed by blocking its acetyltransferase EP300.
UniFORM: Towards Universal Immunofluorescence Normalization for Multiplex Tissue Imaging
Authors: Wang Kunlun , Ait-Ahmad Kaoutar , Kupp Samuel D , Sims Zachary , Cramer Eric , Sayar Zeynep , Yu Jessica , Wong Melissa H. , Mills Gordon B. , Eksi S. Ece , Chang Young Hwan 
Published: December 2024

AbstractMultiplexed tissue imaging (MTI) technologies enable high-dimensional spatial analysis of tumor microenvironments but face challenges with technical variability in staining intensities. Existing normalization methods, including z-score, ComBat, and MxNorm, often fail to account for the heterogeneous, right-skewed expression patterns of MTI data, compromising signal alignment and downstream analyses. We present UniFORM, a non-parametric, Python-based pipeline for normalizing both feature- and pixel-level MTI data. UniFORM preserves marker intensity distribution shapes while maintaining positive population proportions without prior assumptions and uses automated normalization. Benchmarking across two distinct MTI platforms and datasets demonstrates that UniFORM outperforms existing methods in mitigating batch effects while maintaining biological signal fidelity. This is evidenced by improved marker distribution alignment, enhanced kBET scores, and improved downstream analyses such as UMAP visualizations and Leiden clustering. UniFORM also introduces a novel guided fine-tuning option for complex and heterogeneous datasets. Although optimized for fluorescence-based platforms, UniFORM provides a scalable and robust solution for MTI data normalization, enabling accurate and biologically meaningful interpretations.
Bridging the Dimensional Gap from Planar Spatial Transcriptomics to 3D Cell Atlases
Authors: Lin Senlin , Wang Zhikang , Cui Yan , Zou Qi , Han Chuangyi , Yan Rui , Yang Zhidong , Zhang Wei , Gao Rui , Song Jiangning , Zhang Michael Q , Peng Hanchuan , Yu Jintai , Feng Jianfeng , Zhao Yi , Yuan Zhiyuan 
Published: December 2024

AbstractSpatial transcriptomics (ST) has revolutionized our understanding of tissue architecture, yet constructing comprehensive three-dimensional (3D) cell atlases remains challenging due to technical limitations and high cost. Current approaches typically capture only sparsely sampled two-dimensional sections, leaving substantial gaps that limit our understanding of continuous organ organization. Here, we present SpatialZ, a computational framework that bridges these gaps by generating virtual slices between experimentally measured sections, enabling the construction of dense 3D cell atlases from planar ST data. SpatialZ is designed to operate at single-cell resolution and function independently of gene coverage limitations inherent to specific spatial technologies. Comprehensive validation using real 3D ST and independent serial sectioning datasets demonstrates that SpatialZ accurately reconstructs virtual slices while preserving cell identities, gene expression patterns, and spatial relationships. Leveraging the BRAIN Initiative Cell Census Network data, we constructed a 3D hemisphere atlas comprising over 38 million cells, a scale not feasible experimentally. This dense atlas enables unprecedented capabilities, includingin silicosectioning at arbitrary angles, explorations of gene expression across both 3D volumes and surfaces, and 3D mapping of query tissue sections. While currently validated for spatial transcriptomics, the underlying principles of SpatialZ could potentially be adapted for spatial proteomics, spatial metabolomics, and even spatial multi-omics. Validated through internal and external testing, our computationally generated atlas maintains biological accuracy, providing unprecedented resolution of spatial molecular landscapes and demonstrating the potential of computational approaches in advancing 3D ST.
Spawning asynchrony and mixed reproductive strategies in a common mass spawning coral
Authors: Ricardo Gerard F. , Doropoulos Christopher , Babcock Russell C. , Adam Arne A. S. , Buccheri Elizabeth , Robledo Natalia , Uribe-Palomino Julian , Mumby Peter J. 
Published: December 2024

AbstractUnderstanding strategies of organisms that utilise multiple modes of reproduction presents a complex challenge for evolutionary biologists. Platygyra daedalea, a common reef-building coral with unclear reproductive boundaries between morphological species, illustrates these complexities. Here, we evaluate the contribution of these reproductive modes in the coral P. daedalea at Heron Island, on the southern Great Barrier Reef. We tagged and sequenced eighteen coral colonies, representing various degrees of spatial clustering, along a 130-m stretch of shallow reef slope. During spawning, divers collected eggs from each colony and placed them in mesh containers within the spawn slick, allowing free movement of sperm for fertilisation. High levels of spawning asynchrony were observed, potentially indicating distinct genetic clusters within the putative species, which resulted in low fertilisation success (1.5%). Notably, of those fertilised eggs, paternity assignments revealed that all resulting embryos were self-fertilised, with no cross-fertilisation occurring. The adult population showed evidence of two genetically distinct subpopulations, along with levels of spatial autocorrelation and inbreeding. This evidence supports the notion of small breeding populations within larger assemblages, density-dependent population effects, and localised recruitment. Selfing may serve as a reproductive assurance mechanism in such populations, which may be more hierarchically structured than previously thought. Given the lack of evidence for in situ outcrossed fertilisation in this natural coral population during split spawning, it appears that P. daedalea may rely on limited high-density patches of adults for successful cross-fertilisation, utilise atypical modes of reproduction when at low densities, and/or sustain its population through limited progeny.
Auxin and tryptophan trigger common responses in the streptophyte algaPenium margaritaceum
Authors: Carrillo-Carrasco Vanessa Polet , van Galen Martijn , Bronkhorst Jochem , Mutte Sumanth , Sprakel Joris , Hernández-García Jorge , Weijers Dolf 
Published: December 2024

SummaryAuxin is a signaling molecule that regulates multiple processes in the growth and development of land plants. Research gathered from model species, particularlyArabidopsis thaliana, has revealed that the nuclear auxin pathway controls many of these processes through transcriptional regulation. Recently, a non-transcriptional pathway based on rapid phosphorylation mediated by kinases has been described, complementing the understanding of the complexity of auxin-regulated processes. Phylogenetic inferences of both pathways indicate that only some of the components are conserved beyond land plants. This raises fundamental questions about the evolutionary origin of auxin responses and whether algal sisters share mechanistic features with land plants. Here we explore auxin responses in the unicellular streptophyte algaPenium margaritaceum. By assessing physiological, transcriptomic and cellular responses we found that auxin triggers cell proliferation, gene regulation and acceleration of cytoplasmic streaming. Notably, all these responses are also triggered by the structurally related tryptophan. These results identify shared auxin response features among land plants and algae, and suggest that less chemically specific responses preceded the emergence of auxin-specific regulatory networks in land plants.
XRN1 supplies free nucleotides to feed alphavirus replication
Authors: Ruscica Vincenzo , Iselin Louisa , Hull Ryan , Embarc-Buh Azman , Narayanan Samyukta , Palmalux Natasha , Raut Namah , Gu Quan , Chen Honglin , Noerenberg Marko , de Laurent Zaydah R. , Joseph Josmi , Noble Michelle , Igreja Catia , Robertson David L. , Hughes Joseph , Mohammed Shabaz , Pelechano Vicent , Davis Ilan , Castello Alfredo 
Published: December 2024

AbstractSeveral RNA viruses induce widespread degradation of cellular mRNAs upon infection; however, the biological significance and mechanistic details of this phenomenon remain unknown. Here, we make use of a model alphavirus, Sindbis virus (SINV), to fill this knowledge gap. We found that SINV triggers cellular RNA decay through the exonuclease XRN1 and the 5’-to-3’ degradation machinery (5-3DM). These proteins accumulate at viral replication organelles (VROs) and interact with the non-structural protein 1 (nsP1), bringing mRNA degradation into proximity with vRNA synthesis. Our data suggest that monophosphate nucleotides released by cellular RNA decay are recycled through the salvage pathway to feed viral replications. Our work thus reveals a fundamental connection between cellular mRNA degradation and viral replication via nucleotides repurposing.Research highlights5’-3’ RNA decay is essential for the replication of a wide range of viruses.XRN1 directly interacts with transcripts which are degraded during infection.RNA decay factors and salvage pathway members localise to viral factories.Supplying nucleosides to several 5-3DM deficient cells facilitates SINV infection.
The Quorum Sensing regulated sRNA Lrs1 is involved in the adaptation to low iron inPseudomonas aeruginosa
Authors: Panagiotopoulou Dimitra , Catalán Natalia Romo , Wilcox Max , Halliday Nigel , Pantalone Paolo , Lazenby James , Cámara Miguel , Heeb Stephan 
Published: December 2024

AbstractIron is an essential nutrient for microbial growth. The opportunistic pathogenPseudomonas aeruginosacan survive under diverse conditions, including iron-depleted environments with the aid of small non-coding RNAs (sRNAs).P. aeruginosaalso uses three quorum sensing (QS) systems Las, Rhl, and Pqs to coordinate virulence and infection establishment at the population level. This study links the sRNA Lrs1, which is located within the promoter of the Pqs biosynthetic operonpqsABCDE,to iron uptake regulation in theP. aeruginosastrain PAO1-L. Transcriptomics and phenotypic assays indicate that Lrs1 downregulates the production of the siderophore pyochelin but not pyoverdine, and thatlrs1regulation itself is dependent on iron availability. Although Lrs1 has been implicated in a positive feedback loop with the transcriptional regulator LasR in the strain PA14, the present findings indicate that this is not the case in PAO1-L in the tested conditions. Transcription of Lrs1 is dependent on quorum sensing, predominantly on RhlR with an auxiliary effect by PqsE. Furthermore, the Pqs system and phenazine production are modulated by Lrs1 only under iron limitation. This study identifies Lrs1 as a new QS-dependent post-transcriptional regulator of iron uptake and virulence highlighting its importance in environmental adaptation inP. aeruginosa.Graphical abstract
Enhancing nondestructive mass identification via Fourier-transform fluorescence analysis
Authors: Domínguez F. , Yousaf D. , Berrocal J. , Gutiérrez M. J. , Sánchez J. , Block M. , Rodríguez D. 
Published: December 2024

Single-ion mass identification is important for atomic and nuclear physics experiments on ions produced with low yields. Cooling the ion to ultralow temperatures through interaction with a laser-cooled ion will enhance the precision of the measurements. In this paper we present axial-common-mode frequency measurements of balanced and unbalanced Coulomb crystals from the Fourier transform of the fluorescence photons from a Doppler-cooling transition in calcium ions after probing the ion crystal with a five-radio-frequency comb. A single ion nondestructively detected can be used for identification, yielding a mass-resolving power m/ΔmFWHM≈310 from the axial common mode. This identification can be performed from a single measurement within times below 1 s.

Published by the American Physical Society
2024
Identifying Key Parameters for Reducing Recombination Losses at the
p
-
n
Junction of Chalcopyrite Thin-Film Solar Cells
Authors: Elizabeth Amala , Mönig Harry 
Published: December 2024

With a record efficiency of 23.64% achieved in the past year, Cu(In,Ga)Se2 chalcopyrites are the absorbers of choice for thin-film solar cells. In these devices, the p-type chalcopyrite absorber and the n-type window layer form the p-n junction at the interface, which is mediated by a thin buffer layer. Due to its close proximity to the p-n junction, the defect electronic properties of the absorber surface and its interface with the buffer layer are of significant importance to limit recombination losses of photogenerated carriers. Furthermore, the recent surge in the efficiency gains have been achieved with the aid of heavy alkali-metal elements, which are implemented via a postdeposition treatment of the absorber surface. Due to the complex defect physics of chalcopyrite materials, the effects and involved processes of these alkali-metal treatments are so far not well understood. As a fundamental requirement, understanding the intrinsic defect physics of chalcopyrite absorbers and how it is influenced by various surface treatments is of significant importance. In fact, it can provide a basis to develop knowledge-based strategies to reduce recombination losses due to the presence of electronic defect levels in the vicinity of the p-n junction. To experimentally access such defects at the surface, it is essential that the chosen characterization techniques possess high surface sensitivity. Furthermore, due to the pronounced crystallographic lateral inhomogeneities of the polycrystalline chalcopyrite thin films, a high spatial resolution is desirable. A combined analytical approach using scanning probe microscopy and spectroscopy or Kelvin force microscopy and photoelectron spectroscopy methods can provide valuable insights. Despite the extensive literature available on related topics, a consolidated view of the various findings made in this regard and the direct consequences for the device efficiency is still lacking. Our review addresses the significant progress made in understanding the defect electronic properties of the chalcopyrite surface in the past decade. The findings are consolidated into five sections, which illuminate several external sources of electronic defects and surface-passivation procedures. This allows to develop specific strategies to reduce interface recombination losses for device optimization and improved solar-cell efficiencies.

Published by the American Physical Society
2024
Do geopolitical uncertainty and inflation transmit opportunities or threats to green energy consumption?
Authors: Mishra Amritkant , Sahu Pritish Kumar 
Published: December 2024

Purpose
This study aims to examine the impact of geopolitical uncertainty and inflation on green energy consumption. In addition, it aims to reveal the cause-and-effect relationship among these variables.

Design/methodology/approach
The authors exert the panel dynamic ordinary least squares (OLS) approach of Kao and Chiang (2000) and the Granger non-causality method of Dumitrescu and Hurlin (2011). On the other hand, current study relies on the annual time series data of 29 countries from 1985 to 2022.

Findings
The panel dynamic OLS results confirm a long-run relationship between geopolitical uncertainty, inflation and green energy consumption. On the other hand, inflation negatively impacts green energy consumption, with high inflation levels potentially halting the transition. Conversely, geopolitical uncertainty shows no significant effect on green energy use, indicating a reliance on traditional energy sources. Moreover, the current investigation reveals the unidirectional causality from green energy consumption to inflation, while no short-run causality exists from inflation as well as geopolitical uncertainty to green energy consumption in the selected countries.

Research limitations/implications
The authors drew conclusions about the potential impact of geopolitical uncertainty and inflation on green energy uses by considering the macro-level data. However, this investigation further be enhanced by looking at such issues through the micro perspective by understating the thought and perspective of public on the implication of geopolitical uncertainty and inflation on green energy uses. Such micro-level, country-specific study would definitely help us to generate more concrete ideas about such themes.

Practical implications
The empirical findings have important implications for policymakers. Results suggest that high inflation negatively impacts green energy use, so policymakers must consider implementing measures to control the inflation while promoting green energy uses for economic prosperity and environmental sustainability. In the short run, green energy use leads to inflation. Therefore, macroeconomic policymakers can implement various subsidy policies for the general public to mitigate the short-term inflationary impact of green energy use.

Originality/value
This investigation is novel in three ways. First, it explores the impact of geopolitical uncertainty and inflation on green energy use, using Caldara and Iacoviello’s (2022) geopolitical risk index as a proxy of geopolitical uncertainty. Second, it uses panel data econometric analysis, a method that most previous studies have not contemplated for this type of investigation. Finally, by including both advanced and emerging economies, it provides valuable insights for policymakers to develop effective strategies related to green energy consumption for achieving sustainable economic development.
Design of a force-controlled end-effector based on the pneumatic artificial muscle for robotic polishing
Authors: Wu Jianxuan , Song Chenyang , Xiao Sa , Lu Yuankai , Wu Haibin 
Published: December 2024

Purpose
Polishing is a crucial process in mechanical manufacturing. The use of industrial robots to automate polishing is an inevitable trend in future developments. However, current robotic polishing tools are too large to reach inside deep holes or grooves in workpieces. This study aims to use a pneumatic artificial muscle (PAM) as the actuator and designs a force-controlled end-effector to reach inside the deep and narrow areas in the workpiece.

Design/methodology/approach
This approach first addresses the challenge of converting the tensile force generated by the PAM into pushing force through mechanism design. In addition, a dynamics model of the end-effector was established based on the three-element model of the PAM. A combined control strategy was proposed to enhance force control accuracy and adaptability during the polishing process.

Findings
Experiments were conducted on a robotic platform equipped with the proposed end-effector. The experimental results demonstrate that the end-effector can polish the inner end face of holes or grooves with diameters as small as 80 mm and depths reaching 200 mm. By implementing the combined control strategies, the target force tracking error was reduced by 48.66% compared to the use of the PID controller alone.

Originality/value
A new force-controlled end-effector based on the PAM is designed for robotic polishing. According to the experimental result, this end-effector can polish not only the outer surfaces of the workpiece but also the internal surfaces of workpieces with deep holes or grooves specifically. By using the combined control strategy proposed in this paper, the end-effector significantly improves force control precision and polishing quality.
Internal auditors and crisis management: a post-crisis outcome evaluation
Authors: Gao Xinghua , Jaggi Jacob , Yan Han 
Published: December 2024

Purpose
The purpose of the study is to understand how internal auditors in public US universities respond to and manage crises. As part of the post-crisis outcomes evaluation and learning process, the authors examine how internal auditors in public US universities manage their work and resources during the COVID-19 pandemic.

Design/methodology/approach
To motivate the study, the authors analyze internal audit-related information from universities’ audit committee meeting records during the pandemic. Subsequently, the authors conduct semi-structured interviews with chief audit executives (CAEs) and senior internal auditors to learn about their experiences during the pandemic crisis.

Findings
Through the lens of the organizational resilience framework, the authors find that when managing crises, CAEs in US universities play a leading role in providing institutional and emotional support to staff; securing organizational, financial and technical backing from management and audit committees and exercising flexibility in using available resources. Additionally, internal auditors must assess the internal and external environments during crises and adjust their operations accordingly. Increasing professional outreach also helps internal auditors mobilize additional resources in adversity. To thrive in the post-pandemic era, when remote working models become popular, internal auditors need to increase informal communication with management and audit committees and sharpen their data analytics skills.

Originality/value
The study provides an opportunity for internal auditors and their stakeholders to reflect on the wins and losses during the pandemic and prepare for future challenges. The authors propose extending Kimberlin et al.’s (2011) organizational resilience framework by adding a communication factor.