bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sirtuin E deacetylase is required for full virulence of Aspergillus fumigatus
Authors: Wassano Natália S. , da Silva Gabriela B. , Reis Artur H. , A. Gerhardt Jaqueline , Antoniel Everton P. , Akiyama Daniel , Rezende Caroline P. , Neves Leandro X. , Vasconcelos Elton J. R. , de Figueiredo Fernanda L. , Almeida Fausto , de Castro Patrícia A. , Pinzan Camila F. , Goldman Gustavo H. , Paes Leme Adriana F. , Fill Taicia P. , Moretti Nilmar S. , Damasio André 
Published: June 2024

AbstractAspergillus fumigatus represents a public health problem due to the high mortality rate in immunosuppressed patients and the emergence of antifungal-resistant isolates. Protein acetylation is a crucial post-translational modification that controls gene expression and biological processes. The strategic manipulation of enzymes involved in protein acetylation has emerged as a promising therapeutic approach for addressing fungal infections. Sirtuins, NAD+-dependent lysine deacetylases, regulate protein acetylation and gene expression in eukaryotes. However, their role in the human pathogenic fungus A. fumigatus remains unclear. This study constructs six single knockout strains of A. fumigatus and a strain lacking all predicted sirtuins (SIRTKO). The mutant strains are viable under laboratory conditions, indicating that sirtuins are not essential genes. Phenotypic assays suggest sirtuins’ involvement in cell wall integrity, secondary metabolite production, thermotolerance, and virulence. Deletion of sirE attenuates virulence in murine and Galleria mellonella infection models. The absence of SirE alters the acetylation status of proteins, including histones and non-histones, and triggers significant changes in the expression of genes associated with secondary metabolism, cell wall biosynthesis, and virulence factors. These findings encourage testing sirtuin inhibitors as potential therapeutic strategies to combat A. fumigatus infections or in combination therapy with available antifungals.
Immune profiling of age and adjuvant-specific activation of human blood mononuclear cells in vitro
Authors: Schüller Simone S. , Barman Soumik , Mendez-Giraldez Raul , Soni Dheeraj , Daley John , Baden Lindsey R. , Levy Ofer , Dowling David J. 
Published: June 2024

AbstractVaccination reduces morbidity and mortality due to infections, but efficacy may be limited due to distinct immunogenicity at the extremes of age. This raises the possibility of employing adjuvants to enhance immunogenicity and protection. Early IFNγ production is a hallmark of effective vaccine immunogenicity in adults serving as a biomarker that may predict effective adjuvanticity. We utilized mass cytometry (CyTOF) to dissect the source of adjuvant-induced cytokine production in human blood mononuclear cells (BMCs) from newborns (~39-week-gestation), adults (~18-63 years old) and elders (>65 years of age) after stimulation with pattern recognition receptors agonist (PRRa) adjuvants. Dimensionality reduction analysis of CyTOF data mapped the BMC compartment, elucidated age-specific immune responses and profiled PRR-mediated activation of monocytes and DCs upon adjuvant stimulation. Furthermore, we demonstrated PRRa adjuvants mediated innate IFNγ induction and mapped NK cells as the key source of TLR7/8 agonist (TLR7/8a) specific innate IFNγ responses. Hierarchical clustering analysis revealed age and TLR7/8a-specific accumulation of innate IFNγ producing γδ T cells. Our study demonstrates the application of mass cytometry and cutting-edge computational approaches to characterize immune responses across immunologically distinct age groups and may inform identification of the bespoke adjuvantation systems tailored to enhance immunity in distinct vulnerable populations.
High-affinity tuning of single fluorescent protein-type indicators by flexible linker length optimization in topology mutant
Authors: Hara Yusuke , Ichiraku Aya , Matsuda Tomoki , Sakane Ayuko , Sasaki Takuya , Nagai Takeharu , Horikawa Kazuki 
Published: June 2024

AbstractGenetically encoded Ca2+ indicators (GECIs) are versatile for live imaging of cellular activities. Besides the brightness and dynamic range of signal change of GECIs, Ca2+ affinity is another critical parameter for successful Ca2+ imaging, as the concentration range of Ca2+ dynamics differs from low nanomolar to sub-millimolar depending on the celltype and organism. However, ultrahigh-affinity GECIs, particularly the single fluorescent protein (1FP)-type, are lacking. Here, we report a simple strategy that increases Ca2+ affinity through the linker length optimization in topology mutants of existing 1FP-type GECIs. The resulting ultrahigh-affinity GECIs, CaMPARI-nano, BGECO-nano, and RCaMP-nano (Kd = 17–25 nM), enable unique biological applications, including the detection of low nanomolar Ca2+ dynamics, highlighting active signaling cells, and multi-functional imaging with other second messengers. The linker length optimization in topology mutants could be applied to other 1FP-type indicators of glutamate and potassium, rendering it a widely applicable technique for modulating indicator affinity.
Discovery of NSD2 non-histone substrates and design of a super-substrate
Authors: Weirich Sara , Kusevic Denis , Schnee Philipp , Reiter Jessica , Pleiss Jürgen , Jeltsch Albert 
Published: June 2024

AbstractThe human protein lysine methyltransferase NSD2 catalyzes dimethylation at H3K36. It has very important roles in development and disease but many mechanistic features and its full spectrum of substrate proteins are unclear. Using peptide SPOT array methylation assays, we investigate the substrate sequence specificity of NSD2 and discover strong readout of residues between G33 (-3) and P38 (+2) on H3K36. Unexpectedly, we observe that amino acid residues different from natural ones in H3K36 are preferred at some positions. Combining four preferred residues led to the development of a super-substrate which is methylated much faster by NSD2 at peptide and protein level. Molecular dynamics simulations demonstrate that this activity increase is caused by distinct hyperactive conformations of the enzyme-peptide complex. To investigate the substrate spectrum of NSD2, we conducted a proteome wide search for nuclear proteins matching the specificity profile and discovered 22 peptide substrates of NSD2. In protein methylation studies, we identify K1033 of ATRX and K819 of FANCM as NSD2 methylation sites and also demonstrate their methylation in human cells. Both these proteins have important roles in DNA repair strengthening the connection of NSD2 and H3K36 methylation to DNA repair.
Ratiometric nonfluorescent CRISPR assay utilizing Cas12a-induced plasmid supercoil relaxation
Authors: Mohammad Noor , Talton Logan , Dalgan Selen , Hetzler Zach , Steksova Anastasiia , Wei Qingshan 
Published: June 2024

AbstractMost CRISPR-based biosensors rely on labeled reporter molecules and expensive equipment for signal readout. A recent approach quantifies analyte concentration by sizing λ DNA reporters via gel electrophoresis, providing a simple solution for label-free detection. Here, we report an alternative strategy for label-free CRISPR-Cas12a, which relies on Cas12a trans-nicking induced supercoil relaxation of dsDNA plasmid reporters to generate a robust and ratiometric readout. The ratiometric CRISPR (rCRISPR) measures the relative percentage of supercoiled plasmid DNA to the relaxed circular DNA by gel electrophoresis for more accurate target concentration quantification. This simple method is two orders of magnitude more sensitive than the typical fluorescent reporter. This self-referenced strategy solves the potential application limitations of previously demonstrated DNA sizing-based CRISPR-Dx without compromising the sensitivity. Finally, we demonstrated the applicability of rCRISPR for detecting various model DNA targets such as HPV 16 and real AAV samples, highlighting its feasibility for point-of-care CRISPR-Dx applications.
Dynamic metastable vortex states in interacting vortex lines
Authors: Kozlov Sergei , Lesueur Jérôme , Roditchev Dimitri , Feuillet-Palma Cheryl 
Published: June 2024

AbstractThe electron transport in current-biased superconducting nano-bridges is determined by the motion of the quantum vortex confined in the internal disorder landscape. Here we consider theoretically a simple case of a single or two neighbouring linear defects crossing a nano-bridge. The strong anharmonicity of the vortex motion along the defect leads, upon radio frequency (RF) excitation, to fractional Shapiro steps. In the case of two defects, the vortex motion becomes correlated, characterised by metastable states that can be locked to the RF-drive. The lock-unlock process causes sudden voltage jumps and drops in the voltage-current characteristics that can be observed in experiments. We analyse the parameters that promote these metastable dynamic states and discuss their possible experimental realisations.
Discovery of charge order above room-temperature in the prototypical kagome superconductor La(Ru1−xFex)3Si2
Authors: Plokhikh I. , Mielke C. , Nakamura H. , Petricek V. , Qin Y. , Sazgari V. , Küspert J. , Biało I. , Shin S. , Ivashko O. , Graham J. N. , Zimmermann M. v. , Medarde M. , Amato A. , Khasanov R. , Luetkens H. , Fischer M. H. , Hasan M. Z. , Yin J.-X. , Neupert T. , Chang J. , Xu G. , Nakatsuji S. , Pomjakushina E. , Gawryluk D. J. , Guguchia Z. 
Published: June 2024

AbstractThe kagome lattice is an intriguing and rich platform for discovering, tuning and understanding the diverse phases of quantum matter, crucial for advancing modern and future electronics. Despite considerable efforts, accessing correlated phases at room temperature has been challenging. Using single-crystal X-ray diffraction, we discovered charge order above room temperature in La(Ru1−xFex)3Si2(x= 0, 0.01, 0.05), where charge order related to out-of-plane Ru atom displacements appears belowTCO,I  ≃ 400 K. The secondary charge ordered phase emerges belowTCO,II  ≃ 80–170 K. Furthermore, first principles calculations reveal both the kagome flat band and the van Hove point near the Fermi energy in LaRu3Si2, driven by Ru-dz2orbitals. Our results identify LaRu3Si2as the kagome superconductor with the highest known charge ordering temperature, offering a promising avenue for researching room temperature quantum phases and developing related technologies.
Application of simultaneous uncertainty quantification and segmentation for oropharyngeal cancer use-case with Bayesian deep learning
Authors: Sahlsten Jaakko , Jaskari Joel , Wahid Kareem A. , Ahmed Sara , Glerean Enrico , He Renjie , Kann Benjamin H. , Mäkitie Antti , Fuller Clifton D. , Naser Mohamed A. , Kaski Kimmo 
Published: June 2024

Abstract
Background
Radiotherapy is a core treatment modality for oropharyngeal cancer (OPC), where the primary gross tumor volume (GTVp) is manually segmented with high interobserver variability. This calls for reliable and trustworthy automated tools in clinician workflow. Therefore, accurate uncertainty quantification and its downstream utilization is critical.

Methods
Here we propose uncertainty-aware deep learning for OPC GTVp segmentation, and illustrate the utility of uncertainty in multiple applications. We examine two Bayesian deep learning (BDL) models and eight uncertainty measures, and utilize a large multi-institute dataset of 292 PET/CT scans to systematically analyze our approach.

Results
We show that our uncertainty-based approach accurately predicts the quality of the deep learning segmentation in 86.6% of cases, identifies low performance cases for semi-automated correction, and visualizes regions of the scans where the segmentations likely fail.

Conclusions
Our BDL-based analysis provides a first-step towards more widespread implementation of uncertainty quantification in OPC GTVp segmentation.
Research on identification method of abnormal grounding circulating current in single‐core AC submarine cable
Authors: Yang Yuxin , Zhu Yongli , Wang Jinsong , Li Yan 
Published: June 2024

AbstractThe grounding circulation current of the sheath and armour of single‐core AC submarine cables is high during operation, which can easily cause insulation damage and faults. Traditional methods that only monitor the amplitude of grounding circulation current make it difficult to detect defects in the cables, so further research is needed on the mathematical mechanism and detection methods of grounding circulation current. A mathematical model for the capacitance and impedance coupling of a single‐core submarine cable was established, and the influence of factors such as active power, length of armour stripping section, armour resistivity, armour magnetic permeability and grounding resistance on the grounding circulation current was analysed. A method for identifying abnormal grounding circulation current of submarine cables based on the combination of amplitude and phase was proposed.
Unpacking soft power for cities: a theoretical approach
Authors: Sevin Efe 
Published: June 2024

AbstractRecently, there has been a resurgence of cities asserting their presence in the international arena, from engaging in collaborations with global actors to address pressing challenges, to competing to attract investments, visitors, and residents. While existing studies in city diplomacy and city branding offer insights into some of these activities, they often fail to provide a comprehensive account for three main reasons: a lack of dialog between these two fields, activities of cities that transcend the boundaries of either fields, and a disregard for the linkages between nation-states and cities. This article proposes a framework aimed at clarifying the international activities of cities and their relationships with their respective home countries, drawing upon the concept of soft power. The framework has the potential to generate theoretical and practical implications. From a theoretical perspective, it offers a more inclusive analytical lens suitable for integration into future comparative studies examining the international activities of cities. From a practical standpoint, it facilitates strategic planning and policymaking processes.
Norms as instruments of non-violent rivalry? Russian views on the promotion of renewable energy
Authors: Crowley-Vigneau Anne , Baykov Andrey , Kalyuzhnova Yelena 
Published: June 2024

AbstractConstructivists argue that international norms represent shared understandings of appropriate behaviour which become universally accepted after their successful internalisation. However, studies of norm contestation, localisation and death suggest that many norms having originated in the West are perceived elsewhere as instruments used by states to promote their interests abroad. This paper examines whether norms can be a vehicle for non-violent rivalry between states based on a study of the norm on the sustainable energy transition from fossil fuels to renewables. Interviews with representatives of the Russian government, O&G industry and media show that there is a lot of scepticism surrounding this norm because it is geopolitically advantageous to the West and damaging to Russia. The theoretical findings reveal that although grafting a diplomatic initiative onto a mature norm could be effective, this does not mean that norms can easily be created to gain the upper hand in punctual disputes.
Improvement of attitudes and skills using a MOOC about the basic science of climate change
Authors: Ferrari Enzo , Ballegeer Anne-Marie , Corrochano Diego , Fuertes Miguel Ángel , Herrero Teijón Pablo , Delgado Martín María Laura , Andrés Sánchez Santiago , Ruiz Camilo 
Published: June 2024

AbstractEducation needs to be at the forefront of the efforts to mitigate and adapt to Climate Change (CC) effects. We have introduced the Climate Change Competence (C3) to provide a comprehensive route to include the topics of sustainability and CC into the curriculum. This paper analyses how different primary and secondary teachers can improve this competence using a Massive Online Open Course (MOOC) on the basic science of CC. While the improvement in knowledge is expected, we have observed important advances on abilities, and attitudes on CC which are also essential to teach about CC mitigation and adaptation. The present study used a pre-experimental design, with pre-and post-test measurements with a sample of 530 students. While the MOOC focuses on the Science of CC, the participants also advance in attitudes and abilities, revealing an important correlation between these three dimensions of competence. Also, the study reveals that the MOOC improves the C3 in all the participants, but it does in diverse ways for diverse groups.
Analyzing “Jayu” in South Korean presidential rhetoric: a comprehensive study from 1948–2023 with a focus on the Yoon Suk Yeol administration
Authors: Han Seungwoo 
Published: June 2024

AbstractThe current study examines the strategic use of “Jayu” (freedom or liberty) in South Korean politics, with a focus on President Yoon Suk Yeol’s administration, where it symbolizes conservative ideologies and political identity. Employing Natural Language Processing, time-series analysis, and visualization techniques, the research analyzes presidential speeches to explore Yoon’s marked emphasis on Jayu, indicative of a strong conservative allegiance. The findings reveal a significant association between the utilization of Jayu and conservative strategies, underscoring its crucial role in Yoon’s political strategy and its function in garnering support from conservative factions within a polarized political context. Yoon’s discourse, characterized by an extensive use of Jayu, fosters polarization and partisanship, moving away from inclusive dialog. This study illuminates the role of symbolic language in political communication and identity formation, providing insights into the interplay between rhetoric and ideological positions in the intricate political landscape of South Korea.
The WELLBY: a new measure of social value and progress
Authors: Frijters Paul , Krekel Christian , Sanchis Raúl , Santini Ziggi Ivan 
Published: June 2024

AbstractWe introduce the WELLBY, a new measure of social value and progress, which can contribute to the assessment of progress towards the wellbeing of the economy and steer towards activities with the most wellbeing per financial resources invested. After providing a short rationale for the WELLBY, we give a definition and an overview of its properties. We then show how WELLBYs can help decision-makers with ex-ante policy appraisals and deliver a practical example of a youth traineeship programme. We also discuss how coefficients from ex-post wellbeing policy evaluations are now being collected as part of social value banks around the world, feeding into future appraisals. Finally, we illustrate how WELLBYs can be used to measure social progress overall, going beyond GDP.
The criminal law protection mechanism for sustainable development in China – an empirical analysis of environmental pollution crime
Authors: Zhou Ying , Wang Huimin , An Xiaohui 
Published: June 2024

AbstractChina’s environmental criminal law serves as the strongest legal safeguard for the construction of an ecological civilization, revealing the country’s determination and efforts in environmental protection. Prior to 2011, Article 338 of China’s Criminal Law, which is most closely associated with the punishment of polluters, was rarely applied effectively. However, following the revision of Article 338 to address environmental pollution crime in 2011, more than 10,000 cases were filed in just a few years; thus, this law has played a significant role in the smooth advancement of China’s ecological civilization. An empirical analysis of 1600 instances of environmental pollution crime revealed that Chinese courts continue to give precedence to conventional sentencing factors in the enforcement of this criminal law. Despite the vigorous promotion of the ecological civilization concept in recent years within China, its integration into the judiciary process appears inadequate, and the boundaries of environmental pollution crime remain vaguely delineated. Given these circumstances, there is a pressing need for China to enhance its legislative and judicial frameworks regarding environmental criminal law to ensure robust and enduring support for the nation’s sustainable development.
Hearts of Flesh
Authors: Liebermann Rosanne 
Published: June 2024

Abstract
The book of Ezekiel justifies the exilic community’s claim to represent the sole continuation of Yhwh’s people by portraying the Judeans remaining in Judah as having a distinct ethnic identity and therefore bodily makeup. It does so via its presentation of their group history as beginning and ending in Judah, while emphasizing the exiles’ collective memory of entering into their covenant with Yhwh outside of their ancestral land (Ezek 11; 16; 20; 23; 33). This exile-centred collective memory is reinforced by the cultic calendar Ezekiel constructs, which marks sacred time according to specific events in the exilic group’s religious history (e.g., with Sabbaths and Passover). Finally, Ezekiel predicts different futures for the Judeans remaining in Judah and those in exile, revealing how their bodies will diverge yet further according to their distinct fates: monstrification and death for those who remain; purification and life in Yhwh’s image for the exiles.
Personal Resources and Total Pain: Exploring the Multiple Mediation of Fear of Recurrence, Meaning-Making, and Coping in Posttreatment Cancer Patients
Authors: Krok Dariusz , Telka Ewa , Moroń Marcin 
Published: June 2024

Abstract

Background
People with cancer who have completed treatment still experience negative effects, such as an increased risk of experiencing cancer-related pain. Psychological factors tend to influence cancer patients’ ability to cope with pain in various dimensions. Although personal resources are an important factor in buffering total pain, still little is known about the intervening variables and underlying mechanisms.

Purpose
The current study examined the relationship between psychological flexibility, self-esteem, and total pain, while considering fear of recurrence, meaning-making, and coping as potential mediating factors.

Methods
Adults (N = 304) who completed medical treatment (radiotherapy, chemotherapy, and combined therapy) participated in this study. They completed questionnaires measuring the aforementioned variables. Structural equation models were used to examine mediation effects.

Results
Psychological flexibility, and partly self-esteem, were negatively related to the dimensions of total pain. However, to a large extent, these relationships were serially and parallelly mediated by fear of recurrence, meaning-making, and emotion-oriented coping.

Conclusions
Consistent with the meaning-making model, cognitive (meaning-making), and affective (fear of recurrence and emotional coping) factors may be potential mechanisms underlying the association between psychological flexibility, self-esteem, and total pain in posttreatment cancer patients. In this study, they tended to interact in the area of physiological and psychosocial experiences of cancer-related pain.