bluuebunny/crossref_metadata_2025_split huggingface dataset:
DNA superhelicity
Authors: Benham Craig J 
Published: November 2023

Abstract
Closing each strand of a DNA duplex upon itself fixes its linking number L. This topological condition couples together the secondary and tertiary structures of the resulting ccDNA topoisomer, a constraint that is not present in otherwise identical nicked or linear DNAs. Fixing L has a range of structural, energetic and functional consequences. Here we consider how L having different integer values (that is, different superhelicities) affects ccDNA molecules. The approaches used are primarily theoretical, and are developed from a historical perspective. In brief, processes that either relax or increase superhelicity, or repartition what is there, may either release or require free energy. The energies involved can be substantial, sufficient to influence many events, directly or indirectly. Here two examples are developed. The changes of unconstrained superhelicity that occur during nucleosome attachment and release are examined. And a simple theoretical model of superhelically driven DNA structural transitions is described that calculates equilibrium distributions for populations of identical topoisomers. This model is used to examine how these distributions change with superhelicity and other factors, and applied to analyze several situations of biological interest.
Direct visualization of replication and R-loop collision using single-molecule imaging
Authors: Kim Subin , Shin Woo Hee , Kang Yujin , Kim Hongtae , Lee Ja Yil 
Published: November 2023

Abstract
R-loops are three-stranded nucleic acid structures that can cause replication stress by blocking replication fork progression. However, the detailed mechanism underlying the collision of DNA replication forks and R-loops remains elusive. To investigate how R-loops induce replication stress, we use single-molecule fluorescence imaging to directly visualize the collision of replicating Phi29 DNA polymerase (Phi29 DNAp), the simplest replication system, and R-loops. We demonstrate that a single R-loop can block replication, and the blockage is more pronounced when an RNA–DNA hybrid is on the non-template strand. We show that this asymmetry results from secondary structure formation on the non-template strand, which impedes the progression of Phi29 DNAp. We also show that G-quadruplex formation on the displaced single-stranded DNA in an R-loop enhances the replication stalling. Moreover, we observe the collision between Phi29 DNAp and RNA transcripts synthesized by T7 RNA polymerase (T7 RNAp). RNA transcripts cause more stalling because of the presence of T7 RNAp. Our work provides insights into how R-loops impede DNA replication at single-molecule resolution.
Interactome of intact chromatosome variants with site-specifically ubiquitylated and acetylated linker histone H1.2
Authors: Saumer Philip , Scheffner Martin , Marx Andreas , Stengel Florian 
Published: November 2023

Abstract
Post-translational modifications (PTMs) of histones have fundamental effects on chromatin structure and function. While the impact of PTMs on the function of core histones are increasingly well understood, this is much less the case for modifications of linker histone H1, which is at least in part due to a lack of proper tools. In this work, we establish the assembly of intact chromatosomes containing site-specifically ubiquitylated and acetylated linker histone H1.2 variants obtained by a combination of chemical biology approaches. We then use these complexes in a tailored affinity enrichment mass spectrometry workflow to identify and comprehensively characterize chromatosome-specific cellular interactomes and the impact of site-specific linker histone modifications on a proteome-wide scale. We validate and benchmark our approach by western-blotting and by confirming the involvement of chromatin-bound H1.2 in the recruitment of proteins involved in DNA double-strand break repair using an in vitro ligation assay. We relate our data to previous work and in particular compare it to data on modification-specific interaction partners of free H1. Taken together, our data supports the role of chromatin-bound H1 as a regulatory protein with distinct functions beyond DNA compaction and constitutes an important resource for future investigations of histone epigenetic modifications.
TroR is the primary regulator of the iron homeostasis transcription network in the halophilic archaeon Haloferax volcanii
Authors: Martinez Pastor Mar , Sakrikar Saaz , Hwang Sungmin , Hackley Rylee K , Soborowski Andrew L , Maupin-Furlow Julie A , Schmid Amy K 
Published: November 2023

Abstract
Maintaining the intracellular iron concentration within the homeostatic range is vital to meet cellular metabolic needs and reduce oxidative stress. Previous research revealed that the haloarchaeon Halobacterium salinarum encodes four diphtheria toxin repressor (DtxR) family transcription factors (TFs) that together regulate the iron response through an interconnected transcriptional regulatory network (TRN). However, the conservation of the TRN and the metal specificity of DtxR TFs remained poorly understood. Here we identified and characterized the TRN of Haloferax volcanii for comparison. Genetic analysis demonstrated that Hfx. volcanii relies on three DtxR transcriptional regulators (Idr, SirR, and TroR), with TroR as the primary regulator of iron homeostasis. Bioinformatics and molecular approaches revealed that TroR binds a conserved cis-regulatory motif located ∼100 nt upstream of the start codon of iron-related target genes. Transcriptomics analysis demonstrated that, under conditions of iron sufficiency, TroR repressed iron uptake and induced iron storage mechanisms. TroR repressed the expression of one other DtxR TF, Idr. This reduced DtxR TRN complexity relative to that of Hbt. salinarum appeared correlated with natural variations in iron availability. Based on these data, we hypothesize that variable environmental conditions such as iron availability appear to select for increasing TRN complexity.
Cigarette Smoking
Authors: Koenig Harold G. , VanderWeele Tyler J. , Peteet John R. 
Published: November 2023

Abstract
This chapter examines the relationship between religious involvement and cigarette smoking. It first discusses the strength of nicotine addiction and presents information on the prevalence and predictors of cigarette smoking. It then examines predictors of cigarette smoking, such as low socioeconomic status, having family members or friends who smoke, and having a severe mental illness. Next, the effects of cigarette smoking and nicotine-containing products on physical health are examined. Religious teachings on behaviors that adversely affect physical health, such as smoking, are summarized. Research is then reviewed on the relationship between religion and cigarette smoking, first summarizing the results of earlier studies and then exploring research published within the past 10 years. Finally, recommendations for future research are provided, and applications in the clinic and community are suggested.
Diet and Weight
Authors: Koenig Harold G. , VanderWeele Tyler J. , Peteet John R. 
Published: November 2023

Abstract
Obesity is reaching epidemic proportions in the United States and around the world, with serious adverse health consequences. If Americans do not collectively adopt healthier eating habits, it has been estimated that nearly half of the population will be obese in the next 10 years. While genetic, economic, social, and cultural factors all play a role, also important is lack of knowledge, easy access to high-calorie poor nutrition foods, and lack of self-control. The relationship between religiosity, diet, and weight is a complex one, although systematic research suggests that religiosity can play a role in improving diet, controlling weight, and reducing rates of obesity. Religious interventions in faith-based settings are also reviewed. The authors emphasize that much further research is needed to determine how religious resources can be utilized in creating interventions to improve diet, reduce caloric intake, increase exercise, and stop this obesity epidemic.
Wedded to Trouble
Authors: Luthman Johanna 
Published: November 2023

Abstract
The chapter discusses the marriage between Lord Roos and Anne Lake, the unexpected pregnancy of the young countess of Exeter, and Roos’s embassy to Spain. It describes the marriage practices among the nobility and gentry in England and the importance of marriage for adult manhood. The marriage between Roos and Anne Lake was viewed by most as an excellent match between an established noble and an important politician’s family. When the countess of Exeter unexpectedly became pregnant and gave birth to a child in the summer of 1616, rumors flew that her elderly husband might not be the father. The chapter also discusses the ideas that May-December marriages were problematic, potentially leading to the young wife looking outside her marriage for sexual satisfaction, making a cuckold of the elderly husband. Roos was appointed to go as an ambassador to Spain but had trouble raising the needed funds, which leads him to take a disadvantageous loan from his new father-in-law. Lord Roos’s financial difficulties will lead to the beginning of the coming disputes over Roos’s Walthamstow estate. Furthermore, Roos’s Spanish embassy was not as successful as he had hoped.
To the Court of Star Chamber
Authors: Luthman Johanna 
Published: November 2023

Abstract
This chapter describes the four slander suits that were filed in the Court of Star Chamber in the spring and summer of 1618, and the three that continued (one was dismissed). The Lakes and Lady Roos brought two of the cases, and the earl and countess of Exeter the other two. It details the workings of the court of Star Chamber. Slander was becoming a more commonly prosecuted crime in the Jacobean period, and many slander cases were prosecuted in Star Chamber. The families chose this court because it provided maximum exposure for their cases, as the king’s council, their peers, would serve as judges, and because the punishments would be heavier. Lady Roos and the Lakes also did not have sufficient evidence, or royal support, to bring suits for adultery or poisoning, so they chose slander as well. The chapter also outlines the sometimes contentious process of collecting witness testimonies, and the pressure on, and potential rewards for, servants and dependents to testify. The main sources for this chapter include the Star Chamber court cases and letters from courtiers and court observers.
Phronesis
Authors: Kristjánsson Kristján , Fowers Blaine 
Published: November 2023

Abstract
A diverse bandwagon of academics is working with and celebrating the notion of phronesis, or ‘practical wisdom’, as a metacognitive capacity, guiding morally aspirational cognition and action. However, this new phronesis discourse is characterized by frequently unrecognized tensions, lacunae, and ambivalences. The book has five main aims: (1) to set the recently surging interest in phronesis (practical wisdom) in Psychology, Philosophy, Professional Ethics, and Education in an historical and theoretical context; (2) to analyse and elaborate upon Aristotle’s ‘standard model’ of phronesis in a philosophically credible way that allows for a psychologically serviceable and empirically tractable conceptualization; (3) to juxtapose our new Aristotelian phronesis model with a recent consensual model of wisdom in Psychology, and respond to different kinds of scepticism about the usefulness of the phronesis construct; (4) to elicit many practical implications of our model for the development and education of phronesis and its application in areas of professional practice and daily conduct; and (5) to explore the relevance of phronesis in areas that have mostly eluded investigation so far, including the spheres of civic/political virtues and collective (managerial) decision-making. The book works through some relevant puzzles created by the recent phronesis discourse. It ameliorates lacunae in the literature and pushes the research agenda in new, radically cross-disciplinary directions, drawing in equal measure on insights from Psychology, Philosophy, and Education. Through its revised and applied Aristotelianism, the book contributes to debates about the salience of phronesis within Moral Psychology, Moral Philosophy, Moral Education, and Professional Ethics.
A Neo-Aristotelian Phronesis Model and Some Philosophical Alternatives
Authors: Kristjánsson Kristján , Fowers Blaine J. 
Published: November 2023

Abstract
This chapter explains the need to advance on the ‘standard neo-Aristotelian model’ in light of contemporary research. It argues for a four-componential neo-Aristotelian phronesis model allowing for empirical as well as theoretical scrutiny. The four functions are (a) the constitutive function, or the ability to perceive the ethically salient elements of a situation; (b) the integrative function that allows one to choose the best action when conflicting demands arise; (c) the blueprint function or the person’s general understanding of how actions conduce to a flourishing life that motivates and guides a person’s actions, and (d) the emotional regulative function, or the ability to integrate one’s emotional experience with reason to appropriately shape those emotional responses in wise action. The chapter ends by looking at other philosophical accounts of phronesis and scepticism about the need for a phronesis model.
Comparing Our Phronesis Model with the New ‘Common Model’ and Other Psychological Alternatives
Authors: Kristjánsson Kristján , Fowers Blaine J. 
Published: November 2023

Abstract
This chapter compares the Aristotelian phronesis model, from Chapter 2, with the new common model, explained in Chapter 3. The former offers a philosophically grounded, psychologically practicable model of wise (phronetic) decision-making that conceives of morality in realist terms and sees moral considerations as reason-informed. The new common model makes significant progress on previous conceptualizations of wisdom in Psychology by circumscribing the sort of wisdom under scrutiny (as practical, nonabstract), and by foregrounding the role of moral aspirations as grounding the perspectival metacognition at work in wisdom. However, the common model goes awry by lacking vital substantive content. The neo-Aristotelian phronesis model offers a more detailed and overt take on a number of wisdom considerations and variables, carrying substantial explanatory power qua theoretical construct above and beyond the common model. The chapter ends by exploring why other constructs in Psychology, such as metacognition, do not render phronesis redundant.
Educating Phronesis
Authors: Kristjánsson Kristján , Fowers Blaine J. 
Published: November 2023

Abstract
This chapter begins by charting the vagaries of educational discourses on phronesis, and by eliciting some developmental insights from Aristotle. The chapter tries to reconstruct a systematic model of moral development out of those basics. It then elicits various hypotheses about the development of phronesis from the Aristotelian and neo-Aristotelian literature and, hence, lays the foundations of an educational research programme on phronesis. A serviceable conceptualization will need to offer ways to evaluate the educational credibility of each hypothesis in real life, rather than just serving as a new philosophical plaything. The chapter then reviews various findings from the educational literature on phronesis. The fourth section explores some lessons learnt from a study of a phronesis intervention for Police Science students, in particular about the limited role of teaching in the design of such an intervention. The chapter closes with some reflections about the education of civic phronesis.
Can Female Performers Be Heard?
Authors: Luthfa Samina 
Published: November 2023

Abstract
This chapter investigates female theatre actors’ identity formation and their struggles in surviving on stage by using feminist research as an anti-oppressive tool. This chapter presents archival data and life stories of eight female performers of Bangladesh who worked on Dhaka stage from the 1950s till the 2010s. Using a participatory reflexive research method, the author observes that historically women’s gender roles inside the theatre troupes had changed, so did the nature of dignity they hold in the eyes of general people, the theatre community, and their co-workers in their own troupe. Moreover, the amount of abuse or harassment increased, though the nature and type of perpetrators changed. Their accounts reveal that family remains as important in the 2010s as it was in the 1950s in determining how one will survive in theatre and the same goes with gendered roles, body image, or gendered construction of feminine beauty. These narratives also speak a lot about how they strategize and decide on steps to survive and remain active in theatre—their ‘arts of resistance’.
The Enigmatic World of Sadhansanginis
Authors: Chakravarti Sudhir 
Published: November 2023

Abstract
One of the most integral yet little-known practices in baul culture is coupled meditation, in which the male baul commences in sadhana (ascetic praxis) with a female partner, who are called sadhansanginis. The difficulty of the practice’s translatability to a modern, urban culture has led to the rise of many complex questions, including that of the prevalence of patriarchal norms in baul society. Through a sociological study of baul practices, from experiences collected over many years of encounters with sadhansanginis, this chapter aims to examine the complexities of this tradition. Locating baul culture within intersections of gender and caste-based hierarchies, the chapter attempts to shed much needed light on the agency (or lack of it) of the sadhansangini within baul culture.
Living Computers
Authors: Brazma Alvis 
Published: November 2023

Abstract
This book explores life as an information processing phenomenon. I posit that life and the recording of information emerged together inextricably linked and that nothing is as central to life, as its ability to record, communicate, and process information. For most of the last several billion years, almost all nonredundant durable information that has existed on Earth has been stored in DNA. As life on Earth was evolving, information in DNA was accumulating, at least at early stages of evolution. A few hundred thousand years ago, human language emerged, and for the first time, large amounts of information started accumulating also outside DNA. The emergence of language triggered evolutionary mechanisms different from, and faster than biological evolution, namely, cultural evolution. Most likely, information is now growing faster in the world’s libraries and computer clouds than in the genomes of all species on Earth taken together. The emergence of human language was a transition as remarkable as the emergence of life itself. Despite the existence of language and the new means of information recording and processing it enabled, at the current stage of evolution, the information in DNA is indispensable; without information in DNA all cultural information and life itself would disappear soon. But need life be like this? Or could future civilisations, in thousands or millions of years, possibly colonising planets of distant galaxies, be based on entirely different principles? Will there be another transition in which DNA becomes less central? The book is aimed at everybody interested in science and comfortable with elementary mathematics: high-school students, teachers, engineers, medical doctors, and business managers, amongst others. It will also be of interest to students and scholars of a wide range of disciplines, from physics, computing, and biology to social sciences and philosophy.
Communicating Between Auditory Regions and the Rest of the Brain
Authors: Zatorre Robert 
Published: November 2023

Abstract
The auditory dorsal stream consists of a complex set of interconnected regions linking the auditory cortex with the parietal lobe, dorsal premotor cortex, and the dorsolateral prefrontal cortex, among others. These links allow several functional properties to emerge that are critical for music. The ability to manipulate information in working memory depends upon this circuitry and allows musical function like transposition to happen. This same dorsal pathway also provides the interface needed for auditory-motor integration, including the organization of actions in time and space to generate musical sounds, which in turn is related to abstract temporal representations, such as metrical structure. These functions can be thought of in the context of transformations from one domain to another. From a predictive coding perspective, the dorsal stream allows the prediction of when anticipated events will occur.
Gartersnakes of the Beaver Archipelago
Authors: Burghardt Gordon M , Krause Mark A , Placyk Jr John S , . Gillingham James C 
Published: November 2023

Abstract
The Beaver Archipelago is a series of islands in northern Lake Michigan, USA, roughly equidistant from the lower and upper peninsulas of the state of Michigan. Of the eight species of snakes found in the archipelago, prey generalist Common Gartersnakes, Thamnophis sirtalis, are by far the most common, inhabiting both the nearby mainland and all the islands on which snakes are found. The island system and nearby mainland were under glaciers until their retreat about 10,000 years ago, and the islands and the herpetofauna did not form until considerably later. Genetic studies have documented that insular snakes have genes from populations inhabiting both adjacent mainlands. The authors report on morphological, behavioral, and ecological similarities and differences both within and among islands as well as with mainland populations. Generally, adults differ more across the populations than do neonates. Experimental data document that both genetics and developmental plasticity underlie some of the differences found.
Pierre Boulez
Authors: Salem Joseph 
Published: November 2023

Abstract
Part biography, part survey, Pierre Boulez: The Formative Years (1925–1962) explores the creative process of a mercurial musician among an array of interrelated contexts, sketches, and correspondence. As a revisionist history, The Formative Years highlights Boulez’s sensitivity to the negative reception of his works. Despite his reputation as an autodidact, Boulez was reliant on a series of teachers, peers, and mentors to gauge the success of his musical ideas, from his first exploits on the piano through his drafting of Pli selon pli in the early 1960s. He used this feedback to practice continual self-reform. Across his writings and compositions, Boulez revisited old material to reconfigure elements from his past. Over time, his cumulative efforts became the palimpsests of a fragmented self in conflict with his world. A book that both celebrates and critiques its subject, The Formative Years challenges the idea that Boulez was a modernist. As he struggled to first find a voice and later control it, he frequently turned to models such as René Char, Anton Webern, and Stephane Mallarmé. But as his music matured, he found new expressive possibilities in the reiterative techniques of poststructuralism. His most experimental sketches feature recomposed transcriptions of previous works as a means for expanding the expressive boundaries of serialism. The journey evidenced by his sketches forces a reconsideration of serialism’s influence among a host of other postmodern genres.