bluuebunny/crossref_metadata_2025_split huggingface dataset:
Historic breeding practices contribute to germplasm divergence in leaf specialized metabolism and ecophysiology in cultivated sunflower (Helianthus annuus)
Authors: Dowell Jordan A. , Bowsher Alan W. , Jamshad Amna , Shah Rahul , Burke John M. , Donovan Lisa A. , Mason Chase M. 
Published: February 2024

AbstractThe use of hybrid breeding systems to increase crop yields has been the cornerstone of modern agriculture and is exemplified in the breeding and improvement of cultivated sunflower (Helianthus annuus). However, it is poorly understood what effect supporting separate breeding pools in such systems, combined with continued selection for yield, may have on leaf ecophysiology and specialized metabolite variation. Here, we analyze 288 cultivatedH. annuuslines to examine the genomic basis of several specialized metabolites and agronomically important traits across major heterotic groups. Heterotic group identity supports phenotypic divergences between fertility restoring and cytoplasmic male-sterility maintainer lines in leaf ecophysiology and specialized metabolism. However, the divergence is not associated with physical linkage to nuclear genes that support current hybrid breeding systems in cultivatedH. annuus. Further, we identified four genomic regions associated with variation in leaf ecophysiology and specialized metabolism that co-localize with previously identified QTLs in cultivatedH. annuusfor quantitative self-compatibility traits and with SPH-proteins, a recently discovered family of proteins associated with self-incompatibility and self/nonself recognition inPapaver rhoeas(common poppy) with suggested conserved downstream mechanisms among eudicots. Self-compatibility is a derived trait in cultivatedH. annuuswith quantitative variation in selfing success, suggesting that trait linkage to divergent phenotypic traits may have partially arisen as a potential unintended consequence of historical breeding practices. Further work is necessary to confirm the self-incompatibility mechanisms in cultivatedH. annuusand their relationship to the integrative and polygenic architecture of leaf ecophysiology and specialized metabolism in cultivated sunflower.
Unleashing Precision and Freedom in Optical Manipulation: Software-Assisted Real-Time Precision Opto-Control of Intracellular Molecular Activities and Cell Functions
Authors: Dong Bin , Everly R. Mike , Mahapatra Shivam , Carlsen Mark S. , Ma Seohee , Zhang Chi 
Published: February 2024

AbstractThe traditional method in biological science to regulate cell functions often employs chemical interventions, which commonly lack precision in space and time. While optical manipulation offers superior spatial precision, existing technologies are constrained by limitations in flexibility, accuracy, and response time. Here, we present an adaptable and interactive optical manipulation platform that integrates laser scanning, chemical sensing, synchronized multi-laser control, adaptable target selection, flexible decision-making, and real-time monitoring of sample responses. This software-assisted real-time precision opto-control (S-RPOC) platform facilitates automatic target selection driven by optical signals while permitting user-defined manual delineation. It allows the treatment of mobile or stationary targets with varying laser dosages and wavelengths simultaneously at diffraction-limited spatial precision and optimal accuracy. Significantly, S-RPOC showcases versatile capabilities including adaptive photobleaching, comprehensive quantification of protein dynamics, selective organelle perturbation, control of cell division, and manipulation of individual cell behaviors within a population. With its unprecedented spatiotemporal precision and adaptable decision-making, S-RPOC holds the potential for extensive applications in biological science.
Tetrapod terrestrialisation: a weight-bearing potential already present in the humerus of the stem-tetrapod fishEusthenopteron foordi
Authors: Clarac François , Cornille Alexis , Bijl Sifra , Sanchez Sophie 
Published: February 2024

AbstractOur study shows that the von Mises stress, induced by external load on the humerus of Eusthenopteron, dissipates through the cortex, trabeculae and the muscles of the pectoral appendage involved in elevation and protraction. As Eusthenopteron’s microanatomy is similar to that of Devonian tetrapods, we expect them to share the same process of load dissipation and energy absorption through 1) cortical stress distribution; and 2) longitudinal trabecular conduction. Our FE simulations in hypothetical terrestrial conditions demonstrate that this type of microanatomical architecture could withstand the weight of Tiktaalik proportionally to the size of Eusthenopteron in standing posture. This tubular arrangement, including marrow processes originally involved in long-bone elongation, would have acquired a key secondary biomechanical function to increase the resistance and strength of the cancellous bone to external compressive load. As an exaptation, this specific trabecular architecture may have played a major role in the tetrapod land exploration about 400 million years ago.
Evolutionary and biological mechanisms underpinning chitin degradation in aquatic fungi
Authors: Chrismas Nathan , Bird Kimberley , Laundon Davis , Hesketh-Best Poppy , Lieng Chloe , Cunliffe Michael 
Published: February 2024

AbstractFungal biology underpins major processes in ecosystems. The Chytridiomycota (chytrids) is a group of early-diverging fungi, many of which function in ecosystems as saprotrophs processing high molecular weight biopolymers, however the mechanisms underpinning chytrid saprotrophy are poorly understood. Genome sequences from representatives across the group and the use of model chytrids offers the potential to determine new insights into their evolution. In this study, we focused on the biology underpinning chitin saprotrophy, a common ecosystem function of aquatic chytrids. The genomes of chitinophilic chytrids have expanded inventories of glycoside hydrolase genes responsible for chitin processing, complemented with bacteria-like chitin-binding modules (CBMs) that are absent in other chytrids. In the model chitinophilic saprotrophRhizoclosmatium globosumJEL800, the expanded repertoire of chitinase genes is diverse and almost half were detected as proteins in the secretome when grown with chitin. Predicted models of the secreted chitinases indicate a range of active site sizes and domain configurations. We propose that increased diversity of secreted chitinases is an adaptive strategy that facilitates chitin degradation in the complex heterologous organic matrix of the arthropod exoskeleton. Free swimmingR. globosumJEL800 zoospores are chemotactic to the chitin monomer N-acetylglucosamine and accelerate zoospore development when grown with chitin. Our study sheds light on the underpinning biology and evolutionary mechanisms that have supported the saprotrophic niche expansion of some chytrids to utilise lucrative chitin-rich particles in aquatic ecosystems and is a demonstration of the adaptive capability of this successful fungal group.
Spatiotemporal regulation of the hepatocyte growth factor receptor MET activity by sorting nexins 1/2 in HCT116 colorectal cancer cells
Authors: Garcia Delgado Laiyen , Derome Amélie , Longpré Samantha , Giroux-Dansereau Marilyne , Basbous Ghenwa , Lavoie Christine L. , Saucier Caroline , Denault Jean-Bernard 
Published: February 2024

ABSTRACTCumulative research findings support the idea that endocytic trafficking is crucial in regulating receptor signaling and associated diseases. Specifically, strong evidence points to the involvement of sorting nexins (SNXs), particularly SNX1 and SNX2, in the signaling and trafficking of the receptor tyrosine kinase (RTK) MET in colorectal cancer (CRC). Activation of hepatocyte growth factor (HGF) receptor MET is a key driver of CRC progression. In this study, we utilized human HCT116 CRC cells withSNX1andSNX2genes knocked out to demonstrate that their absence leads to a delay in MET entering early endosomes. This delay results in increased phosphorylation of both MET and AKT upon HGF stimulation, while ERK1/2 (extracellular signal-regulated kinases 1 and 2) phosphorylation remains unaffected. Despite these changes, HGF-induced cell proliferation, scattering, and migration remain similar between the parental and theSNX1/2knockout cells. However, in the absence of SNX1 and SNX2, these cells exhibit increased resistance to TRAIL-induced apoptosis. This research underscores the intricate relationship between intracellular trafficking, receptor signaling, and cellular responses and demonstrates for the first time that the modulation of MET trafficking by SNX1 and SNX2 is critical for receptor signaling that may exacerbate the disease.
Dorsal Raphe to Basolateral Amygdala Corticotropin-Releasing Factor Circuit Regulates Cocaine-Memory Reconsolidation
Authors: Ritchie Jobe L. , Qi Shuyi , Soto David A. , Swatzell Sydney E. , Grenz Hope I. , Pruitt Avery Y. , Artimenia Lilia M. , Cooke Spencer K. , Berridge Craig W. , Fuchs Rita A. 
Published: February 2024

ABSTRACTEnvironmental stimuli elicit drug craving and relapse in cocaine users by triggering the retrieval of strong cocaine-related contextual memories. Retrieval can also destabilize drug memories, requiring reconsolidation, a protein synthesis-dependent storage process, to maintain memory strength. Corticotropin-releasing factor (CRF) signaling in the basolateral amygdala (BLA) is necessary for cocaine-memory reconsolidation. We have hypothesized that a critical source of CRF in the BLA is the dorsal raphe nucleus (DR) based on its neurochemistry, anatomical connectivity, and requisite involvement in cocaine-memory reconsolidation. To test this hypothesis, male and female Sprague-Dawley rats received adeno-associated viruses to express Gi-coupled designer receptors exclusively activated by designer drugs (DREADDs) selectively in CRF neurons of the DR and injection cannulae directed at the BLA. The rats were trained to self-administer cocaine in a distinct environmental context then received extinction training in a different context. They were then briefly re-exposed to the cocaine-predictive context to destabilize (reactivate) cocaine memories. Intra-BLA infusions of the DREADD agonist deschloroclozapine (DCZ; 0.1 mM, 0.5 μL/hemisphere) after memory reactivation attenuated cocaine-memory strength, relative to vehicle infusion. This was indicated by a selective, DCZ-induced and memory reactivation-dependent decrease in drug-seeking behavior in the cocaine-predictive context in DREADD-expressing males and females at test compared to respective controls. Notably, BLA-projecting DR CRF neurons that exhibited increased c-Fos expression during memory reconsolidation co-expressed glutamatergic and serotonergic neuronal markers. Together, these findings suggest that the DRCRF→ BLA circuit is engaged to maintain cocaine-memory strength after memory destabilization, and this phenomenon may be mediated by DR CRF, glutamate, and/or serotonin release in the BLA.
Scaffold-Lab: Critical Evaluation and Ranking of Protein Backbone Generation Methods in A Unified Framework
Authors: Zheng Zhuoqi , Zhang Bo , Zhong Bozitao , Liu Kexin , Li Zhengxin , Zhu Junjie , Yu Jinyu , Wei Ting , Chen Hai-Feng 
Published: February 2024

AbstractDe novoprotein design has undergone a rapid development in recent years, especially for backbone generation, which stands out as more challenging yet valuable, offering the ability to design novel protein folds with fewer constraints. However, a comprehensive delineation of its potential for practical application in protein engineering remains lacking, as does a standardized evaluation framework to accurately assess the diverse methodologies within this field. Here, we proposed Scaffold-Lab benchmark focusing on evaluating unconditional generation across metrics like designability, novelty, diversity, efficiency and structural properties. We also extrapolated our benchmark to include the motif-scaffolding problem, demonstrating the utility of these conditional generation models. Our findings reveal thatFrameFlowandRFdiffusionin unconditional generation along withRfdiffusionand GPDL in conditional generation showcased the most outstanding performances. Furthermore, we described a systematic study to investigate conditional generation and applied it to the motif-scaffolding task, offering a novel perspective for the analysis and development of conditional protein design methods. All data and scripts will be available athttps://github.com/Immortals-33/Scaffold-Lab.
Cell circuits underlying nanomaterial specific respiratory toxicology
Authors: Voss Carola , Han Lianyong , Ansari Meshal , Strunz Maximilian , Haefner Verena , Ballester-Lopez Carol , Angelidis Ilias , Mayr Christoph H. , Berthing Trine , Conlon Thomas , Liu Qiongliang , Ren Hongyu , Zhou Qiaoxia , Schmid Otmar , Yildirim Ali Önder , Rehberg Markus , Vogel Ulla , Gote-Schniering Janine , Theis Fabian J. , Schiller Herbert B. , Stoeger Tobias 
Published: February 2024

AbstractNanomaterials emerged as boundless resource of innovation, but their shape and biopersistence related to respiratory toxicology raise longstanding concerns. The development of predictive safety tests for inhaled nanomaterials, however, is hampered by limited understanding of cell type-specific responses. To advance this knowledge, we used single-cell RNA-sequencing to longitudinally analyze cellular perturbations in mice, caused by three carbonaceous nanomaterials of different shape and toxicity upon pulmonary delivery. Focusing on nanomaterial-specific dynamics of lung inflammation, we found persistent depletion of alveolar macrophages by fiber-shaped nanotubes. While only little involvement was observed for alveolar macrophages during the initiation phase, they emerged, together with infiltrating monocyte-derived macrophages, as decisive factors in shifting inflammation towards resolution for spherical nanomaterials, or chronic inflammation for fibers. Fibroblasts, central for fibrosis, sensed macrophage and epithelial signals and emerged as orchestrators of nanomaterial-induced inflammation. Thus, the mode of actions identified in this study will significantly inspire the precision of futurein vitrotesting.Graphical abstract
Whole-Genome Sequencing of Three ExtremophileBacillus sp. Strains Isolated from the Atacama Desert
Authors: Cavanaugh Nicole T , Kumar Girish , Frignani Matteo Couto , Thewedros Nathan , Twahirwa Marcello , Riquelme Carlos , Hudson André O , Chai Yunrong , Godoy-Carter Veronica 
Published: February 2024

AbstractThe Atacama Desert is home to bacteria that use biofilms as a means of protecting themselves against the harsh environment. We cultured and sequenced the genomes of threeBacillus sp. isolates from the soil of the Atacama Desert. This information will inform research in survival mechanisms of eubacteria in the Atacama Desert.
MR-SPLIT: a novel method to address selection and weak instrument bias in one-sample Mendelian randomization studies
Authors: Shi Ruxin , Wang Ling , Burgess Stephen , Cui Yuehua 
Published: February 2024

AbstractMendelian Randomization (MR) is a widely embraced approach to assess causality in epidemiological studies. Two-stage least squares (2SLS) method is a predominant technique in MR analysis. However, it can lead to biased estimates when instrumental variables (IVs) are weak. Moreover, the issue of the winner’s curse could emerge when utilizing the same dataset for both IV selection and causal effect estimation, leading to biased estimates of causal effects and high false positives. Focusing on one-sample MR analysis, this paper introduces a novel method termed as Mendelian Randomization with adaptive Sample-sPLitting with cross-fitting InstrumenTs (MR-SPLIT), designed to address bias issues due to IV selection and weak IVs, under the 2SLS IV regression framework. We show that the MR-SPLIT estimator is more efficient than its counterpart cross-fitting MR (CFMR) estimator. Additionally, we introduce a multiple sample-splitting technique to enhance the robustness of the method. We conduct extensive simulation studies to compare the performance of our method with its counterparts. The results underscored its superiority in bias reduction, effective type I error control, and increased power. We further demonstrate its utility through the application of a real-world dataset. Our study underscores the importance of addressing bias issues due to IV selection in high dimensions and weak IVs in one-sample MR analyses and provides a robust solution to the challenge.
Investigation of the factors driving engineering insurance consumption in China’s construction industry: a hybrid approach
Authors: Zhou Xiaowei , Wang Yousong , Gong Enqin 
Published: February 2024

PurposeGiven the increasing importance of engineering insurance, it is still unclear which specific factors can enhance the role of engineering insurance as a risk transfer tool. This study aims to propose a hybrid approach to identify and analyze the key determinants influencing the consumption of engineering insurance in mainland China.Design/methodology/approachThe empirical analysis utilizes provincial data from mainland China from 2008 to 2019. The research framework is a novel amalgamation of the generalized method of moments (GMM) model, the quantile regression (QR) technique and the random forest (RF) algorithm. This innovative hybrid approach provides a comprehensive exploration of the driving factors while also allowing for an examination across different quantiles of insurance consumption.FindingsThe study identifies several driving factors that significantly impact engineering insurance consumption. Income, financial development, inflation, price, risk aversion, market structure and the social security system have a positive and significant influence on engineering insurance consumption. However, urbanization exhibits a negative and significant effect on the consumption of engineering insurance. QR techniques reveal variations in the effects of these driving factors across different levels of engineering insurance consumption.Originality/valueThis study extends the research on insurance consumption to the domain of the engineering business, making theoretical and practical contributions. The findings enrich the knowledge of insurance consumption by identifying the driving factors specific to engineering insurance for the first time. The research framework provides a novel and useful tool for examining the determinants of insurance consumption. Furthermore, the study offers insights into the engineering insurance market and its implications for policymakers and market participants.
Rethinking higher education in light of the sustainable development goals: results from a workshop and examples of implementation in a medical university
Authors: von Knorring Mia , Karlsson Hanna , Stenwall Elizabeth , Nikkola Matti Johannes , Niemi Maria 
Published: February 2024

Purpose
This study aims to analyse student and teaching staff views on how higher education (HE) can contribute to sustainable development, and to provide examples of how a medical university has adopted the sustainable development goals (SDGs) as part of its institutional strategies and practises.

Design/methodology/approach
The study is based on participant views from a conference, which aimed to identify actions needed for HE to contribute to the SDGs. More than 500 students, teachers and academic leaders participated at workshops to discuss and reflect on the role of higher education institutions (HEIs) in sustainable development. The discussion key points were recorded on flipcharts, and the analysis builds on all written statements from the nine workshops. Based on the findings from the workshop, steering documents and activities of a medical university were identified as examples of implementation.

Findings
Two overarching interdependent themes were identified and indicated a need to rethink the role not only of HE per se but also that of HEIs at large, to meet the challenges of sustainable development. The study also provides an example of how such organizational change can be practically implemented at a medical university, through the establishment of overarching institutional strategies, funding opportunities and external collaborations.

Practical implications
The findings reflect a “bottom-up” call from students and educational staff for HEIs to step up and contribute to systems change – both through a change in pedagogies, as well as through an institution-wide approach and a shift in the role of HEIs in society.

Originality/value
The study is unique in providing an exemplar of the implementation of sustainable development in HE at a specific medical university.
A re-examination of four decades’ deregulation effect on competition and productivity of the US freight rail transportation industry
Authors: Shin Seungjae 
Published: February 2024

PurposeThe purpose of this study is to compare the competition and productivity of the US freight rail transportation industry for the past 41 years (1980 ∼ 2020), which consists of the two periods, before and after the abolishment of the Interstate Commerce Commission (ICC) in 1995.Design/methodology/approachThis study investigates any relationships between the market concentration index values and labor productivity values in the separate two periods, and how the existence of a regulatory body in the freight transportation market impacted the productivity of the freight rail transportation industry by using a Cobb–Douglas production function on annual financial statement data from the US stock exchange market.FindingsThis study found that, after the abolishment of the ICC: (1) the rail industry became less competitive, (2) even if the rail industry had an increasing labor productivity trend, there was a strong negative correlation between the market concentration index and labor productivity and (3) the rail industry’s total factor productivity was decreased.Originality/valueThis study is to find empirical evidence of the effect of the ICC abolishment on the competition and productivity levels in the US freight rail transportation industry using a continuous data set of 41-year financial statements, which is unique compared to previous studies.