bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular regulation of apple and grape ripening: exploring common and distinct transcriptional aspects of representative climacteric and non-climacteric fruits
Authors: Zenoni Sara , Savoi Stefania , Busatto Nicola , Tornielli Giovanni Battista , Costa Fabrizio 
Published: August 2023

Abstract
Fleshy fruits of angiosperms are organs specialized for promoting seed dispersal by attracting herbivores and enticing them to consume the organ and the seeds it contains. Ripening can be broadly defined as the processes serving as a plant strategy to make the fleshy fruit appealing to animals, consisting of a coordinated series of changes in color, texture, aroma, and flavor that result from an intricate interplay of genetically and epigenetically programmed events. The ripening of fruits can be categorized into two types: climacteric, which is characterized by a rapid increase in respiration rate typically accompanied by a burst of ethylene production, and non-climacteric, in which this pronounced peak in respiration is absent. Here we review current knowledge of transcriptomic changes taking place in apple (Malus × domestica, climacteric) and grapevine (Vitis vinifera, non-climacteric) fruit during ripening, with the aim of highlighting specific and common hormonal and molecular events governing the process in the two species. With this perspective, we found that specific NAC transcription factor members participate in ripening initiation in grape and are involved in restoring normal physiological ripening progression in impaired fruit ripening in apple. These elements suggest the existence of a common regulatory mechanism operated by NAC transcription factors and auxin in the two species.
Resonant dynamical friction around a supermassive black hole: analytical description
Authors: Ginat Yonadav Barry , Panamarev Taras , Kocsis Bence , Perets Hagai B 
Published: August 2023

ABSTRACT
We derive an analytical model for the so-called phenomenon of resonant dynamical friction, where a disc of stars around a supermassive black hole interacts with a massive perturber, so as to align its inclination with the disc’s orientation. We show that it stems from a singular behaviour of the orbit-averaged equations of motion, which leads to a rapid alignment of the argument of the ascending node Ω of each of the disc stars, with that of the perturber, Ωp, with a phase difference of 90°. This phenomenon occurs for all stars whose maximum possible $\dot{\Omega }$ (maximized over all values of Ω for all the disc stars) is greater than $\dot{\Omega }_{\rm p}$; this corresponds approximately to all stars whose semi-major axes are less than twice that of the perturber. The rate at which the perturber’s inclination decreases with time is proportional to its mass and is shown to be much faster than Chandrasekhar’s dynamical friction. We find that the total alignment time is inversely proportional to the root of the perturber’s mass. This persists until the perturber enters the disc. The predictions of this model agree with a suite of numerical N-body simulations, which we perform to explore this phenomenon, for a wide range of initial conditions, masses, etc., and are an instance of a general phenomenon. Similar effects could occur in the context of planetary systems, too.
Exploring source region of 3-min slow magnetoacoustic waves observed in coronal fan loops rooted in sunspot umbra
Authors: Rawat Ananya , Gupta Girjesh R 
Published: August 2023

ABSTRACT
Sunspots host various oscillations and wave phenomena like umbral flashes, umbral oscillations, running penumbral waves, and coronal waves. All fan loops rooted in sunspot umbra constantly show a 3-min period propagating slow magnetoacoustic waves in the corona. However, their origin in the lower atmosphere is still unclear. In this work, we studied these oscillations in detail along a clean fan loop system rooted in active region AR 12553 for a duration of 4 h on 2016 June 16 observed by Interface Region Imaging Spectrograph and Solar Dynamics Observatory. We traced foot-points of several fan loops by identifying their locations at different atmospheric heights from the corona to the photosphere. We found presence of 3-min oscillations at foot-points of all the loops and at all atmospheric heights. We further traced origin of these waves by utilizing their amplitude modulation characteristics while propagating in the solar atmosphere. We found several amplitude modulation periods in the range of 9–14, 20–24, and 30–40 min of these 3-min waves at all heights. Based on our findings, we interpret that 3-min slow magnetoacoustic waves propagating in coronal fan loops are driven by 3-min oscillations observed at the photospheric foot-points of these fan loops in the umbral region. We also explored any connection between 3- and 5-min oscillations observed at the photospheric foot-points of these loops and found them to be weakly coupled. Results provide clear evidence of magnetic coupling of the solar atmosphere through propagation of 3-min waves along fan loops at different atmospheric heights.
nautilus: boosting Bayesian importance nested sampling with deep learning
Authors: Lange Johannes U 
Published: August 2023

ABSTRACT
We introduce a novel approach to boost the efficiency of the importance nested sampling (INS) technique for Bayesian posterior and evidence estimation using deep learning. Unlike rejection-based sampling methods such as vanilla nested sampling (NS) or Markov chain Monte Carlo (MCMC) algorithms, importance sampling techniques can use all likelihood evaluations for posterior and evidence estimation. However, for efficient importance sampling, one needs proposal distributions that closely mimic the posterior distributions. We show how to combine INS with deep learning via neural network regression to accomplish this task. We also introduce nautilus, a reference open-source python implementation of this technique for Bayesian posterior and evidence estimation. We compare nautilus against popular NS and MCMC packages, including emcee, dynesty, ultranest, and pocomc, on a variety of challenging synthetic problems and real-world applications in exoplanet detection, galaxy SED fitting and cosmology. In all applications, the sampling efficiency of nautilus is substantially higher than that of all other samplers, often by more than an order of magnitude. Simultaneously, nautilus delivers highly accurate results and needs fewer likelihood evaluations than all other samplers tested. We also show that nautilus has good scaling with the dimensionality of the likelihood and is easily parallelizable to many CPUs.
TDP-1 and FUST-1 co-inhibit exon inclusion and control fertility together with transcriptional regulation
Authors: Taylor Morgan , Marx Olivia , Norris Adam 
Published: August 2023

AbstractGene expression is a multistep process and crosstalk among regulatory layers plays an important role in coordinating gene expression. To identify functionally relevant gene expression coordination, we performed a systematic reverse-genetic interaction screen in C. elegans, combining RNA binding protein (RBP) and transcription factor (TF) mutants to generate over 100 RBP;TF double mutants. We identified many unexpected double mutant phenotypes, including two strong genetic interactions between the ALS-related RBPs, fust-1 and tdp-1, and the homeodomain TF ceh-14. Losing any one of these genes alone has no effect on the health of the organism. However, fust-1;ceh-14 and tdp-1;ceh-14 double mutants both exhibit strong temperature-sensitive fertility defects. Both double mutants exhibit defects in gonad morphology, sperm function, and oocyte function. RNA-Seq analysis of double mutants identifies ceh-14 as the main controller of transcript levels, while fust-1 and tdp-1 control splicing through a shared role in exon inhibition. A skipped exon in the polyglutamine-repeat protein pqn-41 is aberrantly included in tdp-1 mutants, and genetically forcing this exon to be skipped in tdp-1;ceh-14 double mutants rescues their fertility. Together our findings identify a novel shared physiological role for fust-1 and tdp-1 in promoting C. elegans fertility and a shared molecular role in exon inhibition.
Deciphering a global source of non-genetic heterogeneity in cancer cells
Authors: Zhang Jianhan , Han Xu , Ma Liang , Xu Shuhui , Lin Yihan 
Published: August 2023

Abstract
Cell-to-cell variability within a clonal population, also known as non-genetic heterogeneity, has created significant challenges for intervening with diseases such as cancer. While non-genetic heterogeneity can arise from the variability in the expression of specific genes, it remains largely unclear whether and how clonal cells could be heterogeneous in the expression of the entire transcriptome. Here, we showed that gene transcriptional activity is globally modulated in individual cancer cells, leading to non-genetic heterogeneity in the global transcription rate. Such heterogeneity contributes to cell-to-cell variability in transcriptome size and displays both dynamic and static characteristics, with the global transcription rate temporally modulated in a cell-cycle-coupled manner and the time-averaged rate being distinct between cells and heritable across generations. Additional evidence indicated the role of ATP metabolism in this heterogeneity, and suggested its implication in intrinsic cancer drug tolerance. Collectively, our work shed light on the mode, mechanism, and implication of a global but often hidden source of non-genetic heterogeneity.
Outcomes of Combination Platinum-Doublet Chemotherapy and Anti-PD(L)-1 Blockade in KRASG12C-Mutant Non-Small Cell Lung Cancer
Authors: Elkrief Arielle , Ricciuti Biagio , Alessi Joao V , Fei Teng , Kalvin Hannah L , Egger Jacklynn V , Rizvi Hira , Thummalapalli Rohit , Lamberti Giuseppe , Plodkowski Andrew , Hellmann Matthew D , Kris Mark G , Arcila Maria E , Baine Marina K , Rudin Charles M , Lito Piro , Ladanyi Marc , Schoenfeld Adam J , Riely Gregory J , Awad Mark M , Arbour Kathryn C 
Published: August 2023

Abstract

Background
Direct KRASG12C inhibitors are approved for patients with non-small cell lung cancers (NSCLC) in the second-line setting. The standard-of-care for initial treatment remains immune checkpoint inhibitors, commonly in combination with platinum-doublet chemotherapy (chemo-immunotherapy). Outcomes to chemo-immunotherapy in this subgroup have not been well described. Our goal was to define the clinical outcomes to chemo-immunotherapy in patients with NSCLC with KRASG12C mutations.

Patients and Methods
Through next-generation sequencing, we identified patients with advanced NSCLC with KRAS mutations treated with chemo-immunotherapy at 2 institutions. The primary objective was to determine outcomes and determinants of response to first-line chemo-immunotherapy among patients with KRASG12C by evaluating objective response rate (ORR), progression-free survival (PFS), and overall survival (OS). We assessed the impact of coalterations in STK11/KEAP1 on outcomes. As an exploratory objective, we compared the outcomes to chemo-immunotherapy in KRASG12C versus non-G12C groups.

Results
One hundred and thirty eight patients with KRASG12C treated with first-line chemo-immunotherapy were included. ORR was 41% (95% confidence interval (CI), 32-41), median PFS was 6.8 months (95%CI, 5.5-10), and median OS was 15 months (95%CI, 11-28). In a multivariable model for PFS, older age (P = .042), squamous cell histology (P = .008), poor ECOG performance status (PS) (P &lt; .001), and comutations in KEAP1 and STK11 (KEAP1MUT/STK11MUT) (P = .015) were associated with worse PFS. In a multivariable model for OS, poor ECOG PS (P = .004) and KEAP1MUT/STK11MUT (P = .009) were associated with worse OS. Patients with KRASG12C (N = 138) experienced similar outcomes to chemo-immunotherapy compared to patients with non-KRASG12C (N = 185) for both PFS (P = .2) and OS (P = .053).

Conclusions
We define the outcomes to first-line chemo-immunotherapy in patients with KRASG12C, which provides a real-world benchmark for clinical trial design involving patients with KRASG12C mutations. Outcomes are poor in patients with specific molecular coalterations, highlighting the need to develop more effective frontline therapies.
Deuteronomy and Scribes
Authors: Schaper Joachim L. W. 
Published: August 2023

Abstract
This chapter explores the history of research on the functions of scribes in the production of the book of Deuteronomy and provides new observations and suggestions pertaining to a number of aspects of that field of research. In so doing, it discusses new perspectives on the correlation between epigraphic research and biblical exegesis; the theological, social, and political “message” of the scribes; the scribes as an “informational elite”; “deep correspondences” and their expression; and the ideologization of writing (i.e., the conceptualization of God as scribe—and the social reality that is reflected in this conceptualization). The scribes of Deuteronomy are seen as members of the crucial informational elite of the Judahite state, its scribal class, adjusting the traditional authoritative texts and their interpretation to the massive societal changes in the times of Josiah, the Babylonian Exile, and the early Persian period. They thus provided cultural continuity in times of political, social, and economic turmoil.
How Slumming Makes the Slum
Authors: Frenzel Fabian 
Published: August 2023

Abstract
This chapter interrogates the role of slumming, the corporeal or virtual visitation of slums, in the making of slum imaginaries. It focuses on the differences between slumming practices across time, and their effect on the ways slums are perceived. The chapter identifies and compares two significant periods in the history of slumming: the early and contemporary period. It argues that contemporary slumming is to some extant a globalized version of early slumming, using new transport and media technology to expand slumming from a practice largely undertaken within individual cities to a broader international scale. However, this is not just a transformation in scale: contemporary slumming also produces new imaginaries. Slums are no longer predominantly seen as places of despair, but also as places of hope.
Belarusian Underground Culture
Authors: Astrouskaya Tatsiana 
Published: August 2023

Abstract
The chapter dwells on the cultural landscape of Soviet Belarus, one of the national republics of the USSR, most strongly transformed by post-war industrialization and urbanization as well as cultural and national standardization. The focus lies on the late 1960s and the 1970s, the time when the first informal groups of literati and artists got together, and the alternatives to the utopian project of Soviet socialism (which was seen rather as dystopian) were formulated and realized in literature and art. One of the alternatives that are discussed in more detail is the construction of the national counter-utopia, an ideal nation-state relying on partly discovered and revised, partly imagined, and invented historical tradition.
Representation, Identity, and Ethics in Art
Authors: Taylor Paul C. 
Published: August 2023

Abstract
This chapter explores the way several issues in art and the ethics of social identity converge on the notion of representation. It examines four conceptions of artworld representation and argues that attending to them can inform and deepen the practices of making, enjoying, and criticizing art. The aim is not to produce a rigid architectonic of artworld representation but to provide a preliminary mapping of some forms of representation that remain both underexplored by philosophers and relatively undifferentiated in the heat of political debate. This preliminary mapping clarifies the relationship between questions of representation and questions of appropriation, inclusion, and the like. It also begins to clarify the way problems of artworld representation are bound up with political controversies related to social identities like race, gender, class, and national identity.
Authority and Communication
Authors: Cheong Pauline Hope 
Published: August 2023

Abstract
Contentions involving the survivability of religious authority and the uprising of new technologies are historical and recurrent. This chapter discusses the scholarship strand on paradoxes and dialectics, evinced by the dual dynamics of weakening and strengthening of religious authority amid possibilities for conflict and accommodation in our present and digital futures. In doing so, the chapter explicates key communication practices that underpin the constitution of religious authority, summarily described as strategic arbitration, invocation, and branding. Next, in light of intensified challenges in leadership performances, this chapter discusses the dialectical tensions navigated in various contexts—including autonomy-connection, display-concealment, and privilege-disadvantage—to illustrate the precarious durability of religious authority. Finally, this chapter concludes with recommendations for future research in religious authority regarding global and comparative research, intersectional analyses, mixed methods and longitudinal design, and attention to the rise of the internet of things and artificial intelligence to increase ecology validity in fieldwork.
The Tamil Response to Cosmopolitan Languages in Contact
Authors: Annamalai E. , Sriraman T. 
Published: August 2023

Abstract
Tamil, in its long history, has come into contact with various languages. Of them, two cosmopolitan ones (i.e. languages looked upon as models for cultural production), viz. Sanskrit in earlier times, and English more recently, have had a major impact on Tamil, leading to linguistic, literary, and epistemological creation and shifts in worldview. In both cases, translation (in both directions) has played a major part. The impact of Sanskrit and the Sanskrit-related Prakrit, which began well before the Common Era, increased after the Sangam period of Tamil literature, resulting in far-reaching changes in Tamil lexico-semantics, grammatical concepts, and theory of poetics. Contact with English, though different in duration and historical context, has significantly impacted Tamil language and literature and lexical resources in an industrialized and modernized world. It has also brought about a re-evaluation of the canonical past and emergence of new sociolinguistic, literary, and cultural perspectives about Tamil.
Compassion and Care Through Musical Social Emotional Learning
Authors: Edgar Scott N. , D'Ambrosio Kara Ireland , Hackl-Blumstein Elise 
Published: August 2023

Abstract
This chapter addresses the principles of social emotional learning (SEL) and explores strategies and embedded experiences for music classrooms as they embody compassion and care for both teachers and students. Intended to build competence in self-awareness, self-management, social-awareness, relationship management, and responsible decision-making, SEL facilitates reflection and social interactions. Music education classrooms and educators represent fertile ground for implementing caring SEL. When student empowerment drives musical SEL instruction and it is contextually sensitive and culturally relevant, the students’ needs, challenges, and motivations drive all aspects of the curriculum, including SEL implementation. When effectively implemented in the music classroom, SEL can compassionately empower students to amplify their voice, empathize, embrace diversity, and connect with music and each other in profound ways. Finally, we draw connections with universal design for learning (UDL) to frame the necessity for flexibility and meeting individual students’ needs, providing varied means for participation and engagement.
Gene duplications facilitate C4-CAM compatibility in common purslane
Authors: Wang Xiaoliang , Ma Xuxu , Yan Ge , Hua Lei , Liu Han , Huang Wei , Liang Zhikai , Chao Qing , Hibberd Julian M , Jiao Yuannian , Zhang Mei 
Published: August 2023

Abstract
Common purslane (Portulaca oleracea) integrates both C4 and crassulacean acid metabolism (CAM) photosynthesis pathways and is a promising model plant to explore C4-CAM plasticity. Here, we report a high-quality chromosome-level genome of nicotinamide adenine dinucleotide (NAD)-malic enzyme (ME) subtype common purslane that provides evidence for 2 rounds of whole-genome duplication (WGD) with an ancient WGD (P-β) in the common ancestor to Portulacaceae and Cactaceae around 66.30 million years ago (Mya) and another (Po-α) specific to common purslane lineage around 7.74 Mya. A larger number of gene copies encoding key enzymes/transporters involved in C4 and CAM pathways were detected in common purslane than in related species. Phylogeny, conserved functional site, and collinearity analyses revealed that the Po-α WGD produced the phosphoenolpyruvate carboxylase-encoded gene copies used for photosynthesis in common purslane, while the P-β WGD event produced 2 ancestral genes of functionally differentiated (C4- and CAM-specific) beta carbonic anhydrases involved in the C4 + CAM pathways. Additionally, cis-element enrichment analysis in the promoters showed that CAM-specific genes have recruited both evening and midnight circadian elements as well as the Abscisic acid (ABA)-independent regulatory module mediated by ethylene-response factor cis-elements. Overall, this study provides insights into the origin and evolutionary process of C4 and CAM pathways in common purslane, as well as potential targets for engineering crops by integrating C4 or CAM metabolism.
Transcription factors MdMYC2 and MdMYB85 interact with ester aroma synthesis gene MdAAT1 in apple
Authors: Li Li-Xian , Fang Yue , Li Dan , Zhu Zi-Hao , Zhang Ya , Tang Zi-Yu , Li Ting , Chen Xue-Sen , Feng Shou-Qian 
Published: August 2023

Abstract
Volatile esters in apple (Malus domestica) fruit are the critical aroma components determining apple flavor quality. While the exact molecular regulatory mechanism remains unknown, jasmonic acid (JA) plays a crucial role in stimulating the synthesis of ester aromas in apples. In our study, we investigated the effects of methyl jasmonate (MeJA) on the production of ester aroma in apples. MeJA treatment significantly increased ester aroma synthesis, accompanied by the upregulation of several genes involved in the jasmonate pathway transduction. Specifically, expression of the gene MdMYC2, which encodes a transcription factor associated with the jasmonate pathway, and the R2R3-MYB transcription factor gene MdMYB85 increased upon MeJA treatment. Furthermore, the essential gene ALCOHOL ACYLTRANSFERASE 1 (MdAAT1), encoding an enzyme responsible for ester aroma synthesis, showed increased expression levels as well. Our investigation revealed that MdMYC2 and MdMYB85 directly interacted with the promoter region of MdAAT1, thereby enhancing its transcriptional activity. In addition, MdMYC2 and MdMYB85 directly bind their promoters and activate transcription. Notably, the interaction between MdMYC2 and MdMYB85 proteins further amplified the regulatory effect of MdMYB85 on MdMYC2 and MdAAT1, as well as that of MdMYC2 on MdMYB85 and MdAAT1. Collectively, our findings elucidate the role of the gene module consisting of MdMYC2, MdMYB85, and MdAAT1 in mediating the effects of JA and promoting ester aroma synthesis in apples.