bluuebunny/crossref_metadata_2025_split huggingface dataset:
Brine Volatilome Changes Along the Spontaneous Fermentation of Spanish-Style cv. Chalkidiki Green Olives Under High and Low NaCl Conditions
Authors: Alvanoudi Panagiota , Ordoudi Stella A. , Nakas Alexandros , Assimopoulou Andreana N. , Mantzouridou Fani Th. 
Published: September 2023

AbstractTable olives are essential components of the Mediterranean diet. Yet, their contribution to salt intake has prompted efforts to reformulate traditional products via safe interventions, mainly focused on the fermentation step. The volatilomics approach is an important tool to assess the complex table olives fermentation. However, extensive data related to monitoring of volatile organic compounds (VOCs) in manufacturing process of Spanish-style cv. Chalkidiki green table olives are scarce in the literature. The present work systematically examines VOCs profile in brines during spontaneous fermentation of cv. Chalkidiki olives under high (8% w/v) and 50% lower NaCl content using selected combinations of chloride salts (NaCl, KCl, CaCl2) in pilot scale for two consecutive periods. VOCs were determined by headspace solid-phase microextraction coupled with gas chromatography–mass spectrometry. Changes in the population of the dominant microbial groups, pH, and titratable acidity values were also investigated. A total of 56 VOCs were identified, including acids, alcohols, carbonyls, esters, and phenols. Multivariate data analysis explored the links between volatile metabolites, microbial groups, and fermentation stages under different NaCl conditions. The evolution of propanoic acid and 2-butanol was intriguing for monitoring a fermentation dominated by lactic acid bacteria under low NaCl conditions, while 3-methyl-1-butanol was indicative of yeast prevalence arising from seasonal variation and/or high NaCl processing. Τhe important contribution of acetic acid to the overall VOCs profile at a late fermentation stage was typical in low NaCl brines. The complete results could be beneficial for marker-assisted monitoring of the fermentation processes in the future.
What Do (and Don’t) We Know About Self-Compassion? Trends and Issues in Theory, Mechanisms, and Outcomes
Authors: Cha Jane E. , Serlachius Anna S. , Kirby James N. , Consedine Nathan S. 
Published: September 2023

Abstract
Objectives
While self-compassion is increasingly being researched, a clear understanding of what self-compassion is, how it works, and for which outcomes remains elusive. This article summarizes and critically evaluates current theoretical and empirical trends in the self-compassion literature. We provide directions for future research to support a more comprehensive understanding of self-compassion.

Method
This paper systematically evaluates issues in three interrelated areas: (1) over-reliance on a particular conceptualization of self-compassion, (2) a narrow focus on the affective mechanisms as per the general resource model of self-regulation, and (3) the prioritization of intrapersonal outcomes over inter-personal outcomes.

Results
Our analysis suggests that current understandings of what self-compassion is and how it impacts outcomes are limited in several ways. Firstly, self-compassion is almost exclusively operationalized using the Self Compassion Scale, inadvertently constraining how we think about this complex construct. Secondly, a heavy emphasis remains on unmeasured changes in “general resources” as explanatory, while more specific pathways beyond affectivity or resource management are rarely considered. Lastly, intrapersonal outcomes are prioritized over interpersonal or social outcomes, which restricts our understanding of the broader benefits of self-compassion.

Conclusions
To address the limitations, we suggest embracing and assessing multiple conceptualizations of self-compassion, empirically testing a wider range of plausible mediators, and investigating a broader range of outcomes, including those in both interpersonal and social spheres. Ongoing consideration of such issues will facilitate our empirical and theoretical understanding of self-compassion, enabling us to adapt more efficient interventions to benefit a wider group of individuals and our society at large.
‘They couldn’t wait, every day they would say are they coming today?’ Stakeholder perceptions of School–University partnership approaches to science teacher education
Authors: Logan Marianne , Cutter-Mackenzie-Knowles Amy , Lynch David , Osborn Maia 
Published: September 2023

AbstractInitial teacher education programs have been criticised for their failure to deliver classroom-ready graduates. Problems of concern for preservice teachers (PSTs) identified in the literature are insufficient time in the classroom, lack of confidence, inadequate pedagogical knowledge and a theory practice divide. This research examines a school–university partnership approach to science teacher education from the perspective of PSTs, school students, teachers and teacher educators where university tutorials were conducted in a school environment. This research is underpinned by practice architectures theory, it follows collaborative participatory action research methodology using mixed methods of data collection including surveys, interviews and focus groups. The research findings revealed how the program built on PSTs’ pedagogical knowledge and confidence and connected theory with practice. Teachers observed high level student engagement and students building on their prior science knowledge in innovative science lessons. The research provides rich data that illuminate aspects in this school–university partnership approach from a range of perspectives.
Bibliographic review on drought and water level articles
Authors: Abdela Kemal Adem , Fantabil Aragaw , Muleta Dereba , Yohannes Tamirat , Jonah Kazora 
Published: September 2023

AbstractThis bibliographic article on Drought and Water Level examined the relationship between organizations, nations, institutions, authors, references, and publishers. It examined 742 papers from Web of Science at the Nanjing University of Information Science and Technology’s. The total annual publication volume of articles was increased steadily from 2012 to 2021, with China and the United States ranking first and second in terms of publication volume and citations but in quality Switzerland and England were top-level. Institutional-partnership analyses indicated disparities in network density and connections, with the Chinese Academy of Sciences (2012) receiving the highest citations and degrees. The document co-citation analysis (DCA) network was created to improve understanding of the frequency and amplitude of bursts of various publications in separate clusters. The most cited work was J Hydrol (2012), with 302 citations. The analytical tool from CiteSpace collected high-frequency keywords and performed co-occurrence, grouping, and emerging word recognition. Gorges Dam is the most crowded cluster, followed by drought stress. The greatest burst duration and most significant phrase is reservoir (2019), followed by “water quality,” which has a 5 year burst period. Estuaries perform important functions such as water purification and coastal. “Reservoir, water quality, restoration, phytoplankton, temperature, wetland, time series, diversity and carbon dioxide” are the most important terms, while “climate change, drought, water level, impact, growth, variability, response, dynamics, management and model” are the most frequently used keywords. In terms of citations, references, and academic influence, Zhang Q. (2012), the R Core team (2014), and Jappen E. (2015) were the top three contributors. Cook, ER (2013), and Allen, R.G. (2019) ranked first and second in terms of frequency, respectively. In this review work, significant information gaps were discovered in the areas of microbiological dynamics, environmental variables, fen peat incubation, lake water, drought risk reduction, biological ecology, lake acidification, salinity variations, and attribution. Future researchers should focus on these and similar topics, while Chinese and USA authors should concentrate on article quality rather than publishing numbers.
Early harvesting and increasing stubble-cutting height enhance ratoon rice yield
Authors: Chen Yuanwei , Zheng Huabin , Wang Weiqin , Tang Qiyuan 
Published: September 2023

Summary
To clarify the combined effects of the cutting time and cutting height on ratooning ability and rice grain yield of the ratoon crop in the novel ratoon rice cropping, a field experiment was carried out to investigate the combined effects of harvesting time and the stubble-cutting height of the main crop on the growth duration, ratooning ability and grain yield of the ratoon crop. The growth period was shortened by 3.5 days on average when the harvesting time was 10 days ahead of time. On average, the growth duration was prolonged by 7 days per each decrease of 10 cm stubble height. Early harvesting and increasing stubble-cutting height greatly increased the grain yield of the ratoon crop. The highest grain yield was achieved at 10 days after flowering stage and a stubble height of 30 cm, which were 6916 kg·hm−2 for XLY900 and 7262 kg·hm−2 for YY4149, averaged across years. High rice yield of the ratoon crop was mainly depended on panicle numbers and grain-filling percentage, rather than spikelets per panicle. Increasing cutting height and the cutting time of the main crop ahead maintain more stubble biomass and nitrogen content. A significant positive correlation was observed between stubble nitrogen content and tillers-to-stubble ratio (TSR), as well as a significant positive relation was found between panicle-to-stubble ratio and TSR. Therefore, cutting 10 days after flowering stage of the main crop with 30 cm stubble-cutting height enhances ratooning ability due to higher stubble biomass and nitrogen content, and then increases rice yield of the ratoon crop.
Rethinking International Order in Early Modern Europe: Evidence from Courtly Ceremonial
Authors: Bruneau Quentin 
Published: September 2023

AbstractOnce the object of consensus, every aspect of the traditional account of early modern Europe as an anarchic system of sovereign states is now debated—from the existence of sovereign states to the notion of anarchy, and even the European limits of that system. In the context of these disagreements, I develop a new account of international order in early modern Europe grounded in the perceptions of historical actors. I first argue that this can be achieved by studying the tools that practitioners relied on to describe and organize political authority in the world. I subsequently delve into a common, though seldom-studied, tool developed by a group of practitioners known as masters of ceremonies: courtly ceremonial (or ius praecedentiae). I make three substantive claims. First, the political authorities identified in manuals on courtly ceremonial were primarily crowns and republics, but in the later eighteenth century, all eventually came to be described as “states.” Second, all political authorities stood in a hierarchy determined by a specific set of criteria I identify, but new criteria—power and sovereignty—emerged over the course of the eighteenth century. Third, the scope of international order was not self-evident, and it certainly did not have clear “European” limits in the eyes of masters of ceremonies; non-European political authorities could easily be integrated into their orders of precedence. Ultimately, I suggest that IR scholars should reconsider why they study early modern Europe and how they study international orders.
All-optical Compton scattering at shallow interaction angles
Authors: Döpp Andreas , Ta Phuoc Kim , Andriyash Igor A. 
Published: September 2023

All-optical Compton sources combine laser-wakefield accelerators and intense scattering pulses to generate ultrashort bursts of backscattered radiation. The scattering pulse plays the role of a small-period undulator (

${\sim }1\,\mathrm {\mu }{\rm m}$

) in which relativistic electrons oscillate and emit X-ray radiation. To date, most of the working laser-plasma accelerators operate preferably at energies of a few hundreds of megaelectronvolts and the Compton sources developed so far produce radiation in the range from hundreds of kiloelectronvolts to a few megaelectronvolts. However, for such applications as medical imaging and tomography the relevant energy range is 10–100 keV. In this article, we discuss different scattering geometries for the generation of X-rays in this range. Through numerical simulations, we study the influence of electron beam parameters on the backscattered photons. We find that the spectral bandwidth remains constant for beams of the same emittance regardless of the scattering geometry. A shallow interaction angle of

$30^{\circ }$

or less seems particularly promising for imaging applications given parameters of existing laser-plasma accelerators. Finally, we discuss the influence of the radiation properties for potential applications in medical imaging and non-destructive testing.
Fertility and ageing – actuarial perspectives
Authors: Babad Yair , Grenham Dermot , Gutterman Sam 
Published: September 2023

Abstract
Fertility, particularly at its current low level in many developed countries and high level in some less developed countries, is a key factor driving demographic, economic, and societal changes at local, national, and global levels. Population ageing due to low fertility and increasing longevity represents one of the most significant global megatrends and risks. Many countries are already experiencing population decline and rapid growth of their elderly populations, with implications for workforce size, economic development, health and pension schemes, and social security arrangements. Actuaries are well known for their work on mortality and morbidity, but they have rarely considered fertility and its proximate determinants, despite their demographic and economic effects. This paper explores key explanations and outcomes of past and projected future fertility trends, and the implications for actuaries and for political and economic decision-makers.
Analysis of the interplay effect in lung stereotactic ablative radiation therapy based on both breathing motion and plan characteristics
Authors: Ali Asmaa M. , Greenwood Jason B. , Varasteh Mohammad , Esteve Sergio , Jeevanandam Prakash , Göpfert Fabian , Irvine Denise M. , Hounsell Alan R. , McGarry Conor K. 
Published: September 2023

Abstract

Introduction:
Stereotactic ablative radiotherapy (SABR) is susceptible to challenges for tumours affected by intrafraction organ motion. This study aims to investigate the effect of breathing characteristics and plan complexity on the interplay effect.

Methods:
A patient-specific interplay effect evaluation was performed using in-house software with an alpha version of the treatment planning verification software Verisoft (PTW-Freiburg, Germany) on VMAT plans. The OCTAVIUS 4D phantom was used to acquire the static dose distribution, and the simulation approach was utilised to generate the moving dose distribution. The influence of plan complexity, PTV size, number of breaths, and motion amplitudes on the interplay effect were examined. The dose distribution of two extreme phases—end-inhale and end-exhale—was considered using the gamma criteria of 2%/2 mm for the interplay effect evaluation.

Results:
A strong correlation was found between the motion amplitude (p < 0.001) and the NBs (p < 0.001) with the gamma-passing rate. No correlation was found between the gamma-passing rate and the PTV size or plan complexity.

Conclusion:
The simulation tool allowed the analysis of a large number of breathing traces, demonstrating how free-breathing patients, suspected of high interplay, could be selected for other motion management solutions. The simulated cases showed strong interplay effects for long breathing periods with extended motion amplitudes in a small group of patients.
An assessment of model risk in pricing wind derivatives
Authors: Gracianti Giovani , Zhou Rui , Li Johnny Siu-Hang , Wu Xueyuan 
Published: September 2023

AbstractWind derivatives are financial instruments designed to mitigate losses caused by adverse wind conditions. With the rapid growth of wind power capacity due to efforts to reduce carbon emissions, the demand for wind derivatives to manage uncertainty in wind power production is expected to increase. However, existing wind derivative literature often assumes normally distributed wind speed, despite the presence of skewness and leptokurtosis in historical wind speed data. This paper investigates how the misspecification of wind speed models affects wind derivative prices and proposes the use of the generalized hyperbolic distribution to account for non-normality. The study develops risk-neutral approaches for pricing wind derivatives using the conditional Esscher transform, which can accommodate stochastic processes with any distribution, provided the moment-generating function exists. The analysis demonstrates that model risk varies depending on the choice of the underlying index and the derivative’s payoff structure. Therefore, caution should be exercised when choosing wind speed models. Essentially, model risk cannot be ignored in pricing wind speed derivatives.
Interfering with Rac1-activation during neonatal monocyte-macrophage differentiation influences the inflammatory responses of M1 macrophages
Authors: Fu Hang , Zhang Ping , Zhao Xiao-Dong , Zhong Xiao-Yun 
Published: September 2023

AbstractNecrotizing enterocolitis (NEC) is a life-threatening, inflammatory disease affecting premature infants with intestinal necrosis, but the mechanism remains unclear. Neonatal macrophages are thought to play an important role in the pathogenesis of NEC through the production of proinflammatory cytokines. Restriction of cytokine expression in macrophages of NEC tissues may be beneficial. In adult macrophages, interfering with Rac1 has been shown to influence the expression of cytokines. Here, we investigated whether interfering with Rac1 in neonatal macrophages affects their inflammatory responses. First, we found that Rac1-activation was upregulated in the macrophages of rats with NEC model induction compared to controls. The M1 macrophages derived from human neonatal monocytes showed greater Rac1-activation than the M2 macrophages derived from the same monocytes. Inhibition of Rac1-activation by NSC23766 potently reduced the production of proinflammatory cytokines in these M1 macrophages. While neonatal monocytes differentiated into M1 macrophages in vitro, NSC23766 significantly altered cell function during the first six days of incubation with GM-CSF rather than during the subsequent stimulation phase. However, the same effect of NSC23766 was not observed in adult macrophages. Using mass spectrometry, Y-box binding protein 1 (YB1) was identified as being downregulated upon inhibition of Rac1-activation in the neonatal macrophages. Moreover, we found that inhibition of Rac1-activation shortens the poly A tail of PABPC1 mRNA, thereby reducing the translation of PABPC1 mRNA. Consequently, the downregulation of PABPC1 resulted in a reduced translation of YB1 mRNA. Furthermore, we found that TLR4 expression was downregulated in neonatal macrophages, while YB1 expression was reduced. Adding resatorvid (TLR4 signaling inhibitor) to the macrophages treated with NSC23766 did not further reduce the cytokine expression. These findings reveal a novel Rac1-mediated pathway to inhibit cytokine expression in neonatal M1 macrophages and suggest potential targets for the prevention or treatment of NEC.
Supervised discovery of interpretable gene programs from single-cell data
Authors: Kunes Russell Z. , Walle Thomas , Land Max , Nawy Tal , Pe’er Dana 
Published: September 2023

AbstractFactor analysis decomposes single-cell gene expression data into a minimal set of gene programs that correspond to processes executed by cells in a sample. However, matrix factorization methods are prone to technical artifacts and poor factor interpretability. We address these concerns with Spectra, an algorithm that combines user-provided gene programs with the detection of novel programs that together best explain expression covariation. Spectra incorporates existing gene sets and cell-type labels as prior biological information, explicitly models cell type and represents input gene sets as a gene–gene knowledge graph using a penalty function to guide factorization toward the input graph. We show that Spectra outperforms existing approaches in challenging tumor immune contexts, as it finds factors that change under immune checkpoint therapy, disentangles the highly correlated features of CD8+ T cell tumor reactivity and exhaustion, finds a program that explains continuous macrophage state changes under therapy and identifies cell-type-specific immune metabolic programs.
Identification of mobile genetic elements with geNomad
Authors: Camargo Antonio Pedro , Roux Simon , Schulz Frederik , Babinski Michal , Xu Yan , Hu Bin , Chain Patrick S. G. , Nayfach Stephen , Kyrpides Nikos C. 
Published: September 2023

AbstractIdentifying and characterizing mobile genetic elements in sequencing data is essential for understanding their diversity, ecology, biotechnological applications and impact on public health. Here we introduce geNomad, a classification and annotation framework that combines information from gene content and a deep neural network to identify sequences of plasmids and viruses. geNomad uses a dataset of more than 200,000 marker protein profiles to provide functional gene annotation and taxonomic assignment of viral genomes. Using a conditional random field model, geNomad also detects proviruses integrated into host genomes with high precision. In benchmarks, geNomad achieved high classification performance for diverse plasmids and viruses (Matthews correlation coefficient of 77.8% and 95.3%, respectively), substantially outperforming other tools. Leveraging geNomad’s speed and scalability, we processed over 2.7 trillion base pairs of sequencing data, leading to the discovery of millions of viruses and plasmids that are available through the IMG/VR and IMG/PR databases. geNomad is available at https://portal.nersc.gov/genomad.
Multimodal single-cell datasets characterize antigen-specific CD8+ T cells across SARS-CoV-2 vaccination and infection
Authors: Zhang Bingjie , Upadhyay Rabi , Hao Yuhan , Samanovic Marie I. , Herati Ramin S. , Blair John D. , Axelrad Jordan , Mulligan Mark J. , Littman Dan R. , Satija Rahul 
Published: September 2023

AbstractThe immune response to SARS-CoV-2 antigen after infection or vaccination is defined by the durable production of antibodies and T cells. Population-based monitoring typically focuses on antibody titer, but there is a need for improved characterization and quantification of T cell responses. Here, we used multimodal sequencing technologies to perform a longitudinal analysis of circulating human leukocytes collected before and after immunization with the mRNA vaccine BNT162b2. Our data indicated distinct subpopulations of CD8+ T cells, which reliably appeared 28 days after prime vaccination. Using a suite of cross-modality integration tools, we defined their transcriptome, accessible chromatin landscape and immunophenotype, and we identified unique biomarkers within each modality. We further showed that this vaccine-induced population was SARS-CoV-2 antigen-specific and capable of rapid clonal expansion. Moreover, we identified these CD8+ T cell populations in scRNA-seq datasets from COVID-19 patients and found that their relative frequency and differentiation outcomes were predictive of subsequent clinical outcomes.