bluuebunny/crossref_metadata_2025_split huggingface dataset:
Weakly Nonlinear Stability Theory
Authors: Ruban Anatoly I. , Gajjar Jitesh S. B. , Walton Andrew G. 
Published: July 2023

Abstract
Weakly nonlinear stability theory aims at predicting how the growth of the perturbation amplitude affects the value of the critical Reynolds number. The governing equation of weakly nonlinear theory is known as the Landau-Stuart equation. We derive it using the asymptotic technique proposed by Stuart (1960) and Watson (1960). It follows from this equation that fluid flows can be subdivided into two classes, those that are subcritically unstable and those that are supercritically unstable. To the first category belongs, for example, plane Poiseuille flow. For this flow, an increase in the amplitude of the perturbation leads to a decrease of the critical Reynolds number. Contrary to that, the Blasius boundary layer shows a supercritical behaviour where the critical Reynolds number increases with the amplitude of the perturbations. We conclude Chapter 4 with numerical analysis of finite amplitude perturbations that leads to the concept of a neutral surface.
Critique of Colonial Neoliberalism
Authors: Forjwuor Bernard 
Published: July 2023

Abstract
This chapter explores the concept of colonial neoliberalism. This concept is developed at the intersection of two seemingly incommensurable terms: colonialism and neoliberalism. Charting the genealogies of these terms, the chapter shows the lines of entanglements that hold these two concepts together as a mutually reinforcing project. It also demonstrates how self-governance under liberal democracy works to accomplish neoliberal objectives, thus curtailing the legitimacy of ipseity as an essential democratic value. What is legitimized in the absence of ipseity is the neoliberal colonial intrusions that operate as the rationality of power/governmentality that is deployed to regulate postcolonial aspirations and desires. The chapter also demonstrates that what was accomplished through violent colonial oppressive rule is now easily accomplished under these neoliberal colonial terms. The extractive capacity of the West has extended beyond what physical territorial aggrandizement could permit. Unfettered access to resources complements the reproduction of a people that is straight-jacketed into fulfilling the desires of what is now called its development partners.
Historical Background
Authors: Matthew Christopher A. 
Published: July 2023

Abstract
This chapter examines the ancient and modern sources available for the study of Eratosthenes’ experiment to calculate the circumference of the Earth in the third century BC. This chapter also contains a biography of Eratosthenes which looks at his life, education, career, and the city in which he grew up (Cyene). This is followed by an overview of the city of Alexandria and why it became a focus of intellectual enquiry in the ancient world during the politically turbulent times following the death of Alexander the Great through its engagement with its main rival for cultural supremacy in the Greek world—the city of Pergamon. The chapter concludes with an examination of Greek astronomical though up to the time of Eratosthenes. This is done to place the chapters that follow into their correct historical context.
The Circumference
Authors: Matthew Christopher A. 
Published: July 2023

Abstract
This chapter begin with an overview of the findings presented in the work regarding the accuracy of Eratosthenes’ calculation of the circumference of the Earth. It shows that Eratosthenes was able to undertake observations of the shadows cast by sundials, and then apply the details of the ratios gleaned from these observations to calculations of the Earth’s circumference, with a very high level of accuracy. Yet, despite how accurate Eratosthenes’ results were, they were not universally accepted at the time, nor for centuries to come. This chapter concludes with an examination of the influence that his result had on the works of following generations of scholars, astronomers and thinkers, and how it impacted how people saw the world (and their place in it) for the next seventeen centuries. It will also demonstrate how, somewhat ironically, the rejection of Eratosthenes’ accurate result played an important role in one of the most famous feats of the Age of Exploration—a feat which forever changed our understanding of the world.
Nature in the raw, and cooked
Authors: Cutter Asher D. 
Published: July 2023

Abstract
Introduces the topics that get expanded through the remainder of the book: evolution drives biodiversity; evolution can happen fast; humans influence evolution; existing organisms have exotic traits that one might combine together with genetics; humans devised genetic engineering methods using CRISPR-Cas9; and humans stand on the brink of setting loose the new biotechnological evolutionary force of “genetic welding,” as well as the technical and philosophical challenges of such an endeavor. Evolving a viable new and extraordinary species is framed as a biological twin of the Apollo Moon mission, an Artemis Earth mission. Personal anecdotes and examples illustrate amazing exotic creatures that already exist in the world. Summarizes features of the Anthropocene environment, how we humans have led to the world being the way it is, and how humans must define its future.
Evolution’s racetracks
Authors: Cutter Asher D. 
Published: July 2023

Abstract
Demonstrates the rapid speed that evolutionary change can take, using case studies from the laboratory, field experiments, and everyday life. Shows how humans influence evolution to have caused rapid evolution through artificial selection, and use experimental evolution in real time to test the mechanisms of evolution itself. Examples include bacteria and vaccines, lice and insecticides, guppies in tropical streams, Caribbean anoles, and brewer’s yeast in microliter-sized “beer bottles.” The results of evolution can be repeatable in some respects, in terms of both genetic and trait outcomes. Illustrates the fact that evolution can produce rapid change visible in a person’s lifetime, within years, weeks, or even days.
On the origin of species
Authors: Cutter Asher D. 
Published: July 2023

Abstract
Considers what it means to be a species. Shows how natural selection and reproductive strategies influence the formation of reproductive isolation in the form of Dobzhansky-Muller incompatibilities. Explains how genetically distinct biological entities can be reproductively isolated and yet still have conduits to the exchange of DNA, and what this genetic introgression means for genome evolution, the evolution of organismal features, and extinction. Describes hybridization between species, the genetic origins of new species, adaptive radiation, and how we can detect these features of biodiversity. Illustrates speciation concepts with examples from lice, European mice, Iberian snails, Canadian stickleback fish, Caribbean lizards, South American Caenorhabditis nematode roundworms, and American sunflowers.
A midnight coterie of transcendent fauna
Authors: Cutter Asher D. 
Published: July 2023

Abstract
Interweaves the prevailing themes from throughout the book in a forward-looking way. Considers the idea of entire communities of species shaped with the aid of genetic welding. Contrasts creation of new and extraordinary species in the Anthropocene with drastic environmental interventions like solar geoengineering to manage climate change. Revisits ideas about evolutionary engineering in the wild as domesticating nature, creating biological curiosities, and as a societal loss of innocence. Considers the weapons that animals have to defend themselves, including examples from jellyfish, poison birds, wasp stings, and pain-insensitive grasshopper mice. Concludes that humanity will continue to alter evolution’s path across our planet, while withholding advocacy for accelerating the pace of evolution with genetic welding, and promises that there is more change to come.
Nuclear Trust Challenged, 1958–63
Authors: Baylis John , Eames Anthony 
Published: July 2023

Abstract
Less than five years after the signature of the MDA, a new crisis emerged over the US provision of the Skybolt missile to the UK. The controversy settled on the terms of cooperation, Britain’s possession of an independent nuclear deterrent, and how the special status of the Anglo-American nuclear relationship might jeopardize non-proliferation and integration efforts in Europe. Though Skybolt significantly ruptured trust at the political level, it also provided an opportunity for new arrangements to be made concerning the Polaris nuclear submarine and ballistic missile weapons system. Despite the trauma of Skybolt to bilateral relations, the Cuban Missile Crisis and cooperation on other matters suggested that the special relationship remained a unified force in war and diplomacy with Cold War adversaries.
‘Independent’ Deterrence, the MLF, and the Future of Polaris, 1963–9
Authors: Baylis John , Eames Anthony 
Published: July 2023

Abstract
The multilateral force concept threatened Britain’s status as an independent nuclear power. The Atlantic Nuclear Force emerged as the solution, but American ambivalence to Britain’s membership in the nuclear club along with a lack of British support for the US in the Vietnam War led once again to a questioning of the special relationship and a geopolitical drift. More than any prime minister before him, Harold Wilson set out to publicly and privately reassess the importance of the special relationship. However, technical work on Polaris and ABM issues kept alive cooperative working arrangements that would eventually lead to the restoration of the relationship at political levels.
Polaris Improvement
Authors: Baylis John , Eames Anthony 
Published: July 2023

Abstract
Realism took hold in both Washington and Whitehall. While Nixon and Kissinger set out to leverage the Anglo-American nuclear relationship to realize their preferred arrangements to uphold détente, the British under Prime Minister Ted Heath looked to a closer relationship with Europe. Anglo-American nuclear relations were affected by the attempts by France to achieve greater nuclear cooperation with the United States and Heath’s ideas of Anglo-French nuclear cooperation. Differences between the US and the UK were particularly pronounced in the context of arms control and ultimately led the British to pursue the development of their own largely indigenous nuclear warhead.
Conclusion
Authors: Baylis John , Eames Anthony 
Published: July 2023

Abstract
The main conclusion of this study is that the Anglo-American nuclear alliance has been remarkably persistent because of the degree of trust that that has existed between the two countries. That trust, however, has had an ambiguous quality. This ambiguity has been a product of the multi-layered nuclear interactions between American and British society that has allowed mistrust and trust to coexist. In effect, trust in the Anglo-American nuclear alliance has been contingent upon, and strengthened by, each partner’s acceptance that the other may mistrust their intentions for a time, and in specific circumstances, but their broad overarching interests and sentimental attachments are so closely aligned that each country permits mistrust to be framed ambiguously through ‘Understandings’ or informal agreements or for the good of the alliance. It is argued that trust and mistrust are certain to develop in multiple dimensions given the complexity and multi-layered interactions between political leaders, ordinary citizens, scientists and soldiers, cultural elites, and protestors, among others.
Generating a narrative step by step
Authors: Pérez Rafael Pérez y , Sharples Mike 
Published: July 2023

Abstract
This chapter provides a detailed example that illustrates how a computer program can employ the narrative structures defined in Chapter 4 to produce a narrative. Throughout the chapter we explain how the narrative structures are instantiated and how each of the sentences that make up the story arises. We also explain how the use of routines to manipulate text are useful for producing a better-quality output. Then we describe the main characteristics of TALE-SPIN, one of the most well-known story-generators. For instance, we explain that the system represents characters’ goals to meet physical needs, to move around the story-world, to persuade other characters to act in certain ways, and to communicate information. We end with some reflections about the scope and limitations of narrative generation based on problem-solving.
Inspired by the brain
Authors: Pérez Rafael Pérez y , Sharples Mike 
Published: July 2023

Abstract
For years, the brain has been an inspiration for the creation of artificial intelligent systems. In this chapter, we start our study of neural networks by considering the performance of a single artificial neuron. We introduce essential concepts, such as weight, activation function, training, and learning. We describe the main features of a neuron and provide an example that illustrates how it works. For instance, we show how a single neuron is able to detect statistical regularities in a dataset and how those regularities can be employed to correctly classify data that the system has never seen before. We end the chapter describing the main limitation of individual neurons and how such a limitation has been overcome.
Inspired by the brain
Authors: Pérez Rafael Pérez y , Sharples Mike 
Published: July 2023

Abstract
In the 1980s and 1890s, a typical neural network comprised hundreds of elements organized in layers. Nowadays, deep neural networks (DNN) interconnect millions of those artificial neurons. This chapter introduces DNNs. Its objective is to discuss the basic concepts behind DNNs, such as parallel distributed system, training, learning, and transformers, as well as to illustrate how these concepts are used to generate texts. We describe how to design a narrative generator employing this approach. The chapter ends with a summary of some automatic storytellers based on DNNs like GPT-3, some thoughts about the neural-symbolic systems, and a reflection on this approach to narrative generation.
The story we always wanted to tell you
Authors: Pérez Rafael Pérez y , Sharples Mike 
Published: July 2023

Abstract
In this final chapter, we recapitulate the core features of the systems we have studied and draw some general conclusions that provide an overview of the field. We start by summarizing the five techniques studied in this book: templates, problem-solving, planning, engagement and reflection, and statistical methods. We explain how systems can be grouped into different categories, such as audience versus theory. Finally, we reflect on some of the implications for society from the development of automatic narrative generator systems and provide examples, such as how these systems might support intercultural diversity through storytelling, or the role of AI in education.
Immunohistochemical Surrogates for Molecular Stratification in Medulloblastoma
Authors: Chinnam Dheeraj , Saraswati Aastha , Jogunoori Swathi , Verma Aanchal , Kiran Tanvi , Salunke Pravin , Gupta Nalini , Kumar Narendra , Madan Renu , Radotra Bishan Dass , Gupta Kirti 
Published: July 2023

Background:
The WHO classification of central nervous system neoplasms (2016) recognized 4 histologic variants and genetically defined molecular subgroups within medulloblastoma (MB). Further, in the 2021 classification, new subtypes have been provisionally added within the existing subgroups reflecting the biological diversity. YAP1, GAB1, and β-catenin were conventionally accepted as surrogate markers to identify these genetic subgroups.

Objectives:
We aimed to stratify MB into molecular subgroups using 3 immunohistochemical markers. TP53 mutation was also assessed in Wingless (WNT), and Sonic Hedgehog (SHH) subgroups. Demographic profiles, imaging details, and survival outcomes were compared within these molecular subgroups.

Patients and methods:
Our cohort included 164 MB cases diagnosed over the last 10 years. The histologic variants were identified on histology, and tumors were molecularly stratified using YAP1, GAB1, and β-catenin. Further, TP53 mutation was assessed using immunohistochemical in WNT and SHH subgroups. The clinical details and survival outcomes were retrieved from the records, and the mentioned correlates were evaluated statistically.

Results:
The age ranged from 1 to 52 years with M:F ratio of 2:1. Group 3/group 4 constituted the majority (48.4%), followed by SHH (45.9%) and WNT subgroups (5.7%). Desmoplastic/nodular and MB with extensive nodularity had the best survival, whereas large cell/anaplastic had the worst. The follow-up period ranged from 1 to 129 months. The best outcome was observed for the WNT subgroup, followed by the SHH subgroup; group 3/group 4 had the worst. Among the SHH subgroup, TP53 mutant tumors had a significantly poorer outcome compared with SHH-TP53 wildtype.

Conclusions:
Molecular stratification significantly contributes to prognostication, and a panel of 3 antibodies is helpful in stratifying MB into its subgroups in centers where access to advanced molecular testing is limited. Our study reinforces the efficacy of incorporating this cost-effective, minimal panel into routine practice for stratification. Further, we propose a 3-risk stratification grouping, incorporating morphology and molecular markers.
TcZC3HTTP, a regulatory element that contributes toTrypanosoma cruzicell proliferation
Authors: Alves Romagnoli Bruno Accioly , Rodrigues Lucena Aline Castro , Freire Eden Ribeiro , da Rocha Isadora Filipaki Munhoz , Alves Lysangela Ronalte. , Goldenberg Samuel 
Published: July 2023

AbstractPost-transcriptional regulation of gene expression is a critical process for adapting and survivingTrypanosoma cruzi, a parasite with a complex life cycle. RNA binding proteins (RBPs) are key players in this regulation, forming ribonucleoprotein complexes (mRNPs) and RNA granules that control transcript stability, localization, degradation, and translation modulation. Understanding the specific roles of individual RBPs is crucial for unraveling the details of this regulatory network. In this study, we generated null mutants of the TcZC3HTTP gene, a specific RBP in the Trypanosoma family, characterized by a C3H zinc finger and a DNAJ domain associated with RNA and protein binding, respectively. Through cell growth assays, we demonstrated that the absence of TcZC3HTTP or the expression of an additional tagged version significantly impacted epimastigote growth, indicating its contribution to cell proliferation. TcZC3HTTP was found to associate with mRNAs involved in cell cycle and division in epimastigotes, while nutritionally stressed parasites exhibited associations with mRNAs coding for other RBPs and rRNA. Furthermore, our analysis of TcZC3HTTP protein partners revealed the presence of several enzymes during normal growth conditions, whereas starvation conditions enriched ribosomal proteins and other RBPs. This study provides insights into the post-transcriptional regulation of gene expression inT. cruzi, highlighting the role of TcZC3HTTP as an RBP involved in cell proliferation and uncovering its versatile functions in different cellular contexts.ImportanceUnderstanding howTrypanosoma cruzi, the causative agent of Chagas disease, regulates gene expression is crucial for developing targeted interventions. In this study, we investigated the role of TcZC3HTTP, an RNA binding protein, in post-transcriptional regulation. Our findings demonstrate that TcZC3HTTP is essential for the growth and proliferation of epimastigotes, a stage of the parasite’s life cycle. We identified its associations with specific mRNAs involved in cell cycle and division and its interactions with enzymes and other RBPs under normal and starvation conditions. These insights shed light on the regulatory network underlying gene expression inT. cruziand reveal the multifaceted functions of RBPs in this parasite. Such knowledge enhances our understanding of the parasite’s biology and opens avenues for developing novel therapeutic strategies targeting post-transcriptional gene regulation inT. cruzi.
Systematic mapping and modeling of 3D enhancer-promoter interactions in early mouse embryonic lineages reveal regulatory principles that determine the levels and cell-type specificity of gene expression
Authors: Murphy Dylan , Salataj Eralda , Di Giammartino Dafne Campigli , Rodriguez-Hernaez Javier , Kloetgen Andreas , Garg Vidur , Char Erin , Uyehara Christopher M. , Ee Ly-sha , Lee UkJin , Stadtfeld Matthias , Hadjantonakis Anna-Katerina , Tsirigos Aristotelis , Polyzos Alexander , Apostolou Effie 
Published: July 2023

ABSTRACTMammalian embryogenesis commences with two pivotal and binary cell fate decisions that give rise to three essential lineages, the trophectoderm (TE), the epiblast (EPI) and the primitive endoderm (PrE). Although key signaling pathways and transcription factors that control these early embryonic decisions have been identified, the non-coding regulatory elements via which transcriptional regulators enact these fates remain understudied. To address this gap, we have characterized, at a genome-wide scale, enhancer activity and 3D connectivity in embryo-derived stem cell lines that represent each of the early developmental fates. We observed extensive enhancer remodeling and fine-scale 3D chromatin rewiring among the three lineages, which strongly associate with transcriptional changes, although there are distinct groups of genes that are irresponsive to topological changes. In each lineage, a high degree of connectivity or “hubness” positively correlates with levels of gene expression and enriches for cell-type specific and essential genes. Genes within 3D hubs also show a significantly stronger probability of coregulation across lineages, compared to genes in linear proximity or within the same contact domains. By incorporating 3D chromatin features, we build a novel predictive model for transcriptional regulation (3D-HiChAT), which outperformed models that use only 1D promoter or proximal variables in predicting levels and cell-type specificity of gene expression. Using 3D-HiChAT, we performed genome-widein silicoperturbations to nominate candidate functional enhancers and hubs in each cell lineage, and with CRISPRi experiments we validated several novel enhancers that control expression of one or more genes in their respective lineages. Our study comprehensively identifies 3D regulatory hubs associated with the earliest mammalian lineages and describes their relationship to gene expression and cell identity, providing a framework to understand lineage-specific transcriptional behaviors.HIGHLIGHTS-Cell lines representing early embryonic lineages undergo drastic enhancer remodeling and fine-scale 3D chromatin reorganization-Highly interacting 3D hubs strongly enrich for highly expressed, cell-type specific and essential genes-3D chromatin features greatly improve prediction of cell-type specific gene expression compared to 1D promoter features-In silicoand experimental perturbations identify novel enhancers regulating the expression of two or more genes in early embryonic lineages