bluuebunny/crossref_metadata_2025_split huggingface dataset:
Morphological changes of larvae and pupae of Lucilia sericata (Diptera: Calliphoridae) reared at two temperatures and on three food types
Authors: Bambaradeniya Tharindu Bandara , Magni Paola Annarosa , Dadour Ian Robert 
Published: February 2024

Abstract
Determining the minimum postmortem interval (minPMI) from an entomological perspective relies mainly on development data recorded for various species of flies collected from a crime scene or suspicious death. This study focused on the larval and pupal development of Lucilia sericata (Meigen), with an emphasis on the changes of the external morphology of the puparium and its pupal content throughout the duration of metamorphosis. Colonies of L. sericata were reared on 3 types of swine tissue (skeletal muscle, liver tissue, and heart tissue) at 2 different temperature regimes; 24 ± 1 °C and 30 ± 1 °C. The overall developmental time, larval width and length, and inner and outer pupal morphology changes were observed and recorded. The results show that: (i) temperature significantly influenced overall development time, as well as changes in larval width and length, but this effect was not dependent on tissue type; (ii) larval development duration was longest on heart tissue, and shortest on skeletal muscle for both temperatures; and (iii) pupation was longest for larvae reared on skeletal muscle at 24 ± 1 °C, and on liver tissue at 30 ± 1 °C, while those larvae reared on liver tissue at 24 ± 1 °C and heart tissue at 30 ± 1 °C had the shortest pupation period. A seven-character checklist plus 4 landmark stages were developed comprising the external morphology of the puparium and pupal content changes of L. sericata. In conclusion, the study provides larval and pupal development timetables, as well as checklists and photo guides for pupal character development that may be useful for future postmortem determinations.
G-quadruplex-mediated genomic instability drives SNVs in cancer
Authors: Richl Tilmann , Kuper Jochen , Kisker Caroline 
Published: February 2024

Abstract
G-quadruplex (G4s) DNA structures have been implicated in inducing genomic instability and contributing to cancer development. However, the relationship between G4s and cancer-related single nucleotide variants (cSNVs) in clinical settings remains unclear. In this large-scale study, we integrated experimentally validated G4s with genomic cSNVs from 13480 cancer patients to investigate the spatial association of G4s with the cellular cSNV landscape. Our findings demonstrate an increase in local genomic instability with increasing local G4 content in cancer patients, suggesting a potential role for G4s in driving cSNVs. Notably, we observed distinct spatial patterns of cSNVs and common single nucleotide variants (dbSNVs) in relation to G4s, implying different mechanisms for their generation and accumulation. We further demonstrate large, cancer-specific differences in the relationship of G4s and cSNVs, which could have important implications for a new class of G4-stabilizing cancer therapeutics. Moreover, we show that high G4-content can serve as a prognostic marker for local cSNV density and patient survival rates. Our findings underscore the importance of considering G4s in cancer research and highlight the need for further investigation into the underlying molecular mechanisms of G4-mediated genomic instability, especially in the context of cancer.
DNA-PK controls Apollo’s access to leading-end telomeres
Authors: Sonmez Ceylan , Toia Beatrice , Eickhoff Patrik , Matei Andreea Medeea , El Beyrouthy Michael , Wallner Björn , Douglas Max E , de Lange Titia , Lottersberger Francisca 
Published: February 2024

Abstract
The complex formed by Ku70/80 and DNA-PKcs (DNA-PK) promotes the synapsis and the joining of double strand breaks (DSBs) during canonical non-homologous end joining (c-NHEJ). In c-NHEJ during V(D)J recombination, DNA-PK promotes the processing of the ends and the opening of the DNA hairpins by recruiting and/or activating the nuclease Artemis/DCLRE1C/SNM1C. Paradoxically, DNA-PK is also required to prevent the fusions of newly replicated leading-end telomeres. Here, we describe the role for DNA-PK in controlling Apollo/DCLRE1B/SNM1B, the nuclease that resects leading-end telomeres. We show that the telomeric function of Apollo requires DNA-PKcs’s kinase activity and the binding of Apollo to DNA-PK. Furthermore, AlphaFold-Multimer predicts that Apollo’s nuclease domain has extensive additional interactions with DNA-PKcs, and comparison to the cryo-EM structure of Artemis bound to DNA-PK phosphorylated on the ABCDE/Thr2609 cluster suggests that DNA-PK can similarly grant Apollo access to the DNA end. In agreement, the telomeric function of DNA-PK requires the ABCDE/Thr2609 cluster. These data reveal that resection of leading-end telomeres is regulated by DNA-PK through its binding to Apollo and its (auto)phosphorylation-dependent positioning of Apollo at the DNA end, analogous but not identical to DNA-PK dependent regulation of Artemis at hairpins.
Processivity and specificity of histone acetylation by the male-specific lethal complex
Authors: Kiss Anna E , Venkatasubramani Anuroop V , Pathirana Dilan , Krause Silke , Sparr Aline Campos , Hasenauer Jan , Imhof Axel , Müller Marisa , Becker Peter B 
Published: February 2024

Abstract
Acetylation of lysine 16 of histone H4 (H4K16ac) stands out among the histone modifications, because it decompacts the chromatin fiber. The metazoan acetyltransferase MOF (KAT8) regulates transcription through H4K16 acetylation. Antibody-based studies had yielded inconclusive results about the selectivity of MOF to acetylate the H4 N-terminus. We used targeted mass spectrometry to examine the activity of MOF in the male-specific lethal core (4-MSL) complex on nucleosome array substrates. This complex is part of the Dosage Compensation Complex (DCC) that activates X-chromosomal genes in male Drosophila. During short reaction times, MOF acetylated H4K16 efficiently and with excellent selectivity. Upon longer incubation, the enzyme progressively acetylated lysines 12, 8 and 5, leading to a mixture of oligo-acetylated H4. Mathematical modeling suggests that MOF recognizes and acetylates H4K16 with high selectivity, but remains substrate-bound and continues to acetylate more N-terminal H4 lysines in a processive manner. The 4-MSL complex lacks non-coding roX RNA, a critical component of the DCC. Remarkably, addition of RNA to the reaction non-specifically suppressed H4 oligo-acetylation in favor of specific H4K16 acetylation. Because RNA destabilizes the MSL-nucleosome interaction in vitro we speculate that RNA accelerates enzyme-substrate turn-over in vivo, thus limiting the processivity of MOF, thereby increasing specific H4K16 acetylation.
Novel mechanisms of diversity generation in Acinetobacter baumannii resistance islands driven by Tn7-like elements
Authors: Correa Alberto , Shehreen Saadlee , Machado Laura Chacon , Thesier Jordan , Cunic Lille M , Petassi Michael T , Chu Joshua , Kapili Bennett J , Jia Yu , England Kevin A , Peters Joseph E 
Published: February 2024

Abstract
Mobile genetic elements play an important role in the acquisition of antibiotic and biocide resistance, especially through the formation of resistance islands in bacterial chromosomes. We analyzed the contribution of Tn7-like transposons to island formation and diversification in the nosocomial pathogen Acinetobacter baumannii and identified four separate families that recognize different integration sites. One integration site is within the comM gene and coincides with the previously described Tn6022 elements suggested to account for the AbaR resistance island. We established Tn6022 in a heterologous E. coli host and confirmed basic features of transposition into the comM attachment site and the use of a novel transposition protein. By analyzing population features within Tn6022 elements we identified two potential novel transposon-encoded diversification mechanisms with this dynamic genetic island. The activities of these diversification features were confirmed in E. coli. One was a novel natural gain-of-activity allele that could function to broaden transposition targeting. The second was a transposon-encoded hybrid dif-like site that parasitizes the host dimer chromosome resolution system to function with its own tyrosine recombinase. This work establishes a highly active Tn7-like transposon that harnesses novel features allowing the spread and diversification of genetic islands in pathogenic bacteria.
Reactions to a Hypothetical Ban of Open-System Electronic Cigarettes Among People Who Currently Use Electronic Cigarettes
Authors: Soule Eric K , Mayne Shannon , Snipes William , Guy Mignonne C , Breland Alison , Fagan Pebbles 
Published: February 2024

Abstract

Introduction
Policies limiting electronic cigarette (ECIG) device and liquid characteristics have been considered to prevent dependence potential and youth product appeal. “Open-system” ECIGs allow people to adjust device and liquid characteristics, which may undermine these policies. This study examined anticipated reactions to a policy prohibiting the sale of open-system ECIG devices in the United States using concept mapping.

Methods
In 2020, adults who reported ECIG use in the past 30 days (n = 70; 45.1% women; mean age = 33.0, SD = 10.6) recruited from a research registry of individuals from across the United States provided statements into a shared list that completed a prompt: “If open-system vaping devices were no longer sold in the US and only closed-system vaping devices were available, what is a specific reaction or response you would have?” at a study website. Participants rated statements (1–7) on how true the statements were for them. Multidimensional scaling and hierarchical cluster analyses were used to identify thematic clusters. Mean ratings of statements were calculated and compared based on the type of ECIG used and current cigarette smoking status.

Results
Participants generated 85 unique statements. The analysis identified eight themes that were organized into two broad groups. The first group of five clusters described behavioral responses to the hypothetical policy (Loopholes, Switch to Closed-System ECIGs, Legal Approaches to Use Open-System ECIGs, ECIG Use Cessation, Switch to non-ECIG Products). The second group of three clusters described psychological responses to the hypothetical policy (Closed-System ECIG Cons, Psychological Responses, Policy Outcome Concerns).

Conclusions
While a ban on open-system ECIG devices may have positive impacts on public health, policy loopholes, and consumer behaviors may undermine the policy. Efforts to support policy enforcement could increase policy effectiveness.

Implications
Open-system electronic cigarettes (ECIGs) that allow people who use ECIGs to modify ECIG device and liquid characteristics may limit the effectiveness of policies that establish product standards which attempt to limit nicotine delivery and flavor content in ECIG liquids. This study identified predicted reactions to a hypothetical policy prohibiting the sale of open-system ECIGs in the United States. Results suggest that people who use ECIGs may view a policy prohibiting open-system ECIGs unfavorably, but would be willing to use closed-system ECIGs. However, many ECIG users may attempt to find loopholes in the policy or alternative sources to purchase open-system ECIGs if open-systems were banned. Future research should identify strategies for tobacco regulatory policy enforcement to increase effectiveness.
Why Study Logic?
Authors: Migotti Mark 
Published: February 2024

Abstract
This chapter expounds and defends a Peircean thesis that has yet to receive the attention it deserves: the thesis that there is a distinctly and illuminatingly intimate connection between the question what is logic? and the questions why and when is it worth studying? The first half of the chapter deals mainly with the bearing on this topic of the relationship between logic and experience, and on the scope of logic, including a discussion of the status of the Pragmatic maxim as a principle of logic. The second half examines the bearing on the topic of Peirce’s universal categories and the relationship between logic and mathematics.
Peirce’s Theories of Generalized Propositions
Authors: Stjernfelt Frederik 
Published: February 2024

Abstract
The chapter will cover the mature theories of propositions that Peirce develops in his intense theoretical thrust of 1902–1906, with a brief introduction about propositions through his earlier development. The chapter’s focus will be on the generalizations that the notion of proposition undergoes in the period mentioned, and the resulting prelinguistic, multimodal theory of propositions with a conclusion about its current relevance.
Diagrammatic Thinking, Diagrammatic Representations, and the Moral Economy of Nineteenth-Century Science
Authors: Ambrosio Chiara 
Published: February 2024

Abstract
This chapter examines Peirce’s work on and with diagrams and places it in a historical and historiographical context. The chapter shows that Peirce’s philosophical reflections on diagrammatic representations and diagrammatic thinking are greatly enriched when placed explicitly in dialogue with the scientific practice of the time and considered from the perspective of what historians of science have characterized as its “moral economy.” It argues that diagrams and diagrammatic practices, as they emerged and consolidated throughout Peirce’s lifetime, were the shared common ground over which an ever-expanding community of scientists negotiated their reasonings and that debates over validity, rigor, perspicuity, and communicability were as much about issues of reliable representation as they were about the reliability and standing of scientists themselves. Peirce was right at the center of these debates, and his philosophical writings on diagrams, as well as his ambitious program for an innovative system of diagrammatic logic, reflect his active participation in them.
Diagrams, Semiosis, and Peirce’s Metaphor
Authors: Jappy Tony 
Published: February 2024

Abstract
Peirce’s concept of the icon provides an innovative theoretical background to the understanding of metaphor, of the media it is communicated through, and of the intentionalities determining it. However, his evolving conception of signs threatened to cancel advances he had made in 1903, when he introduced a highly original definition of metaphor as one of three hypoicons, or subclasses of the icon. Developments in the semiotics potentially undermining this new approach were the redefinition of the subclass of the icon previously identified as metaphor and the ineligibility of the icon–index–symbol division to function as a stage in the very process of sign-production, namely, semiosis. The chapter first contextualizes and illustrates the definition of metaphor of 1903; it then reviews significant developments in the semiotics in the 1905–1906 period; finally, it proposes a form of mediatization as one means of reconciling two seemingly distinct conceptions of the sign.
Peirce on Biology
Authors: Kull Kalevi 
Published: February 2024

Abstract
This chapter provides (1) a brief account of Peirce’s own statements on biological issues; (2) a short account of the usage of Peirce’s ideas in semiotic biology, (a) before 1990 and (b) after 1990; and (3) a brief review of points that have appeared in biosemiotic literature as critical on applications of some of Peirce’s concepts in biosemiotics. Selecting only the statements in which Peirce explicitly speaks about biology, the chapter observes a more emergentist take than can be concluded from canonical readings of Peirce.
Pragmatic Clarification
Authors: Bergman Mats 
Published: February 2024

Abstract
Although the principal aim of Peirce’s pragmatism seems self-evident—that is, “to render ideas clear”—a closer look at his various articulations and uses of the maxim of pragmatism reveals a more nuanced picture, with several objectives in play. To back up this claim, this chapter sets out from a brief discussion of the provenance of pragmatic elucidation in Peirce’s thought, drawing attention to the significance of the context of inquiry in the work of clarification. Turning to the question of what the Peircean method is supposed to make clear, it is argued that it primarily targets the conceptual constituent of signs. Then, three aims of conceptual clarification, labeled elimination, definition, and development, are identified. These considerations bear upon the largely neglected question of whether Peirce’s method of pragmatism is best construed as a form of “Socratic midwifery,” a tool for clearing the way for inquiry proper, or the kind of investigation that is fueled by genuine doubt and aims at settlement of belief or habit-change. Qualifying Peirce’s assertion that “the maxim of Pragmatism does not bestow a single smile upon beauty, upon moral virtue, or upon abstract truth,” the chief conclusion of the chapter is that at least some uses of the maxim of pragmatism can plausibly be construed as forms of melioristic inquiry.
Peirce on Kant’s Refutation of Idealism
Authors: Gava Gabriele 
Published: February 2024

Abstract
This chapter analyzes two short texts in which Peirce sketches out an anti-skeptical argument inspired by Kant’s refutation of idealism. The chapter will first consider why Peirce found Kant’s argument interesting and promising, given that it is often regarded as problematic and unsuccessful. It will then briefly reconstruct Kant’s refutation, highlighting its most problematic passages. Moreover, since Peirce’s own version of the argument relies on Kant’s views regarding the temporal structure of consciousness, the chapter will explain how Peirce tackles this issue in “The Law of Mind.” Finally, the chapter considers Peirce’s own anti-skeptical argument and examines whether and how it can be seen as appropriating Kant’s strategy.
Charles S. Peirce and the Feeling of Understanding
Authors: de Regt Herman C. D. G. 
Published: February 2024

Abstract
In two early and classic papers, “The Fixation of Belief” and “How to Make Our Ideas Clear,” Peirce draws attention to the evolutionary biology of humans and how it might have repercussions for the way our beliefs and feelings relate to the results of inquiry, even if that inquiry is scientific. We find relevant pragmatist ideas suggesting that the feeling of understanding generated by scientific explanations is not a reliable indicator for thinking our beliefs are true. This offers a new way to criticize the currently widely supported contextual theory of scientific understanding. Surprisingly, the feeling of understanding might be an evolutionary bias leading to pseudoscientific beliefs. Peirce’s two classic papers continue to be valuable resources to help us grasp the way humans manage their beliefs and feelings.
A Science Like Any Other
Authors: Dea Shannon 
Published: February 2024

Abstract
This chapter argues that a Peircean philosophy of sex offers a nonreductionist approach to sex as a biological category. The chapter surveys traditional biological accounts of sex categories and several social constructivist accounts of sex. It then provides an overview of Peirce’s scholastic realism and his ethics of inquiry. While Peirce regarded the distinction between the sexes as a rare “polar distinction,” the chapter works to recover the nuanced view of sex that Peirce ought to have adopted had he extended his scholastic realism to reproductive biology. Ultimately, the Peircean account offered treats sex differences as norms expressed as bimodal distributions. The chapter concludes by illustrating some applications of this Peircean philosophy of sex and gesturing to those that we can yet barely imagine.
Scientific Pride and Metaphysical Prejudice
Authors: Mayorga Rosa 
Published: February 2024

Abstract
Metaphysicians and physicists both share the proud desire to understand the world and all the things in it, to fully comprehend the nature of reality. Almost one hundred years after it was proposed, quantum theory has radically transformed the science of physics, inviting a conception of reality that is drastically at odds with our most rooted metaphysical convictions. A scientist and metaphysician extraordinaire, Charles Peirce (1839–1914) was singularly poised to recognize some of the “metaphysical prejudices” about the world that quantum theory, developed years later, has revealed. This chapter proposes to trace how Peirce’s realism, inspired by the thirteenth-century Franciscan monk John Duns Scotus (c. 1266–1308) and adapted for a reconceived scientific metaphysics, parallels some of the familiar enigmas posed by quantum physics in the early twenty-first century.
The Philosophical Relevance of Peirce’s Historical Studies
Authors: Viola Tullio 
Published: February 2024

Abstract
The chapter explores the different uses of history that emerge from Peirce’s writings and asks to what extent history, from a Peircean perspective, is relevant to philosophy. It starts by looking at the emergence of Peirce’s interest in history as part and parcel of his polymathic profile. It goes on to analyze history’s role in the development of Peirce’s evolutionary account of the human mind. Finally, it explores the relationship between history and logic. Peirce was interested both in exploring history’s bearing on the investigation of logical questions and in employing his logical theories to elaborate a methodology of historical inquiry.
Peirce’s Thwarted Career
Authors: Misak Cheryl 
Published: February 2024

Abstract
This chapter traces the sad history of Peirce’s career in academia. This brilliant philosopher and logician struggled to get a job and then didn’t manage to hold onto it. I show that there was considerable self-harm involved but also suggest that, nonetheless, history must judge America’s great early institutions of higher education—Harvard and Johns Hopkins—as failing to nurture one of the finest talents of American thought.
Peirce’s Formal and Material Categories in Phenomenology
Authors: Atkins Richard Kenneth 
Published: February 2024

Abstract
Peirce’s preferred name for the science of phenomenology is phaneroscopy. He regards phaneroscopy as primarily an observational and classificatory science. Its aim is to analyze the phaneron (whatsoever may come before the mind howsoever) and to classify its constituents. Peirce recognizes at least two different sets of categories according to which the phaneron’s constituents may be classified. These are the formal, quantitative categories and the material, qualitative categories. He devotes most of his energies to pursuing the hypothesis that the formal categories by which we classify the phaneron’s constituents are to be based on the basic forms of predicates. This chapter explains what phaneroscopy is, why it is of importance, and Peirce’s work on the formal and material categories.
The Vicissitudes of Experience
Authors: Houser Nathan 
Published: February 2024

Abstract
Peirce’s conception of experience is framed by his doctrine of categories and is inextricably linked with his related conceptions of consciousness, perception, and semiosis. The aim of this chapter is to consider experience from these different perspectives and to contribute toward a more integrated general Peircean theory of experience. It is suggested that Peirce’s analysis of semiosis and his classification of signs is an analysis and classification of possible experiential links between world and mind or, more strictly, between sensation and perception. Peirce viewed himself as an empiricist, but his empiricism is framed in a realist ontology and epistemology that distinguishes it from more usual nominalist approaches.