bluuebunny/crossref_metadata_2025 huggingface dataset:
Does One Size Fit All? Cultural Perspectives on School Motivation
Authors: McInerney Dennis M.
Published: January 2023

Early theorizing on what motivates students to learn was largely based on Western conceptualizations and specifically on a “one-size-fits-all” belief that what works is relatively universal. However, the one-size-fits-all notion fails to explain diversity in motivation and achievement. Every perspective on motivation should be looked at for variability in meaning and relevance within particular social and cultural settings. The critical importance of culture and the cultural setting adds new richness and complexity to theorizing on motivation in school settings. Overall, the essay briefly describes the transitioning of theory from Western-based, relatively monocultural theories of motivation to a richer understanding of motivation by interrogating theoretical perspectives and practical applications through a cultural lens.
Some Motivations Make Us Happier Than Others
Authors: Sheldon Kennon M.
Published: January 2023

To answer, “What is good motivation?”, consider research on “the pursuit of happiness.” Good motivation brings happiness, while bad motivation does not. Happiness (subjective well-being or SWB) is easily measured: it involves having lots of positive moods, few negative moods, and much satisfaction with life. By tracking SWB over time, one can discover which motivated behaviors bring happiness and which do not. The former tends to be “eudaimonic” motivations, involving compassion, service, humility, excellence, and the like. Eudaimonic motivations satisfy peoples’ psychological needs, bringing SWB as one side effect. Another question is to ask why people sometimes persist in non–happiness-producing motivations.
Do We Sometimes Surrender Our Good Motivation for Bad?
Authors: Wigfield Allan
Published: January 2023

Researchers characterize motivation as varying in both quantity and quality. Yet, depending on individuals’ intentions and the outcomes of actions, high-quantity and high-quality motivations can be thought of as either good or bad. Even good motivations in terms of both quantity and quality, such as high self-efficacy and high task value, can become bad motivations when done in the service of negative outcomes. Many similar examples may be found in popular television show, politics, and everyday life. Similarly, as the author of this essay explains, whether a motivation can be considered good or bad further depends on culture and the particular situation.
Finding the Second Wind
Authors: Usher Ellen L.
Published: January 2023

Many people feel as though their actions are primarily the result of external demands or involuntary impulses over which they have little control. This essay takes a different approach by considering the many ways in which people can and do influence their own motivation and behavior. People exercise control over their motivational states by organizing and selecting their thoughts, feelings, environments, and actions. They reflect on their performances, and they revise strategies that will make success more likely. These self-regulatory processes make it possible for people to enhance their own motivation. Even in dire circumstances, people always have some degree of control over their lives.
Exploring the Boundaries Between Motivation, Cognition, and Emotion
Authors: Alexander Patricia A.
Published: January 2023

The answer to whether motivation can be distinguished from cognition and emotion differs depending on whether one is a researcher, a theorist, or a teacher. A researcher conceptualizes and then operationalizes motivation, cognition, and emotion to either highlight or minimize areas of distinction. A theorist models the interrelations among cognition, emotion, and motivation in nuanced ways that allow for both their convergence and divergence. A teacher is far less concerned about whether it is possible to draw clear empirical and theoretical distinctions among these three constructs. Instead, the teacher is far more invested in harnessing the collective power of these three concepts to promote students’ learning and academic development.
Creating a Motivating Learning Environment
Authors: Alexander Patricia A.
Published: January 2023

The question, “How do we motivate people,” stirs up several preliminary questions: Is it actually possible to motivate others? And, motivate people to do what? This essay accepts the challenge of the question to provide four guiding principles in how to motivate students to learn deeply, think critically and analytically, and justify their understandings. First, to motivate learners effectively, build on what already moves, excites, or interests students. Second, take time to establish a meaningful link between the content to be taught and the students. Third, ensure that students’ backgrounds, personal experiences, and beliefs are valued within the learning environment and woven into instruction. Fourth, treat students as unique individuals with varied strengths and differences, and provide opportunities for choice, self-direction, and self-expression that play to those strengths and differences.
How to Foster Motivation?
Authors: Vansteenkiste Maarten , Soenens Bart
Published: January 2023

Teachers, leaders, parents, and sport coaches often rely on their intuition to motivate others. Although sometimes effective, intuition can also misguide motivating agents. Intuition needs to be sharpened by theoretical insights. Grounded in self-determination theory, this essay presents a motivating compass featuring a variety of motivating (e.g., guiding, attuning) and demotivating (e.g., domineering, abandoning) approaches situated in a circular structure. Whereas some practices in the model relate to greater engagement and high-quality motivation because of their need-satisfying properties, other practices come with a motivational cost and predict disengagement because of their need-frustrating effect. This motivating compass provides concrete indications of how to motivate others.
Mirrors of the Divine
Authors: Cain Emily R.
Published: January 2023

This book brings into focus how four influential late ancient authors—Tertullian of Carthage, Clement of Alexandria, Gregory of Nyssa, and Augustine of Hippo—employ language of vision and of mirrors in their discursive struggles to construct Christian agency, identity, and epistemology. These authors span from the second through fourth centuries CE in both Eastern and Western Christianity, and this book analyzes their theological writings on vision and knowledge of God to explore how they pieced together rival and contradictory theories of sight to shape their cosmologies, theologies, subjectivities, genders, and discursive worlds. The different theories of vision partly answered the question of how we see; but more, the differences around vision and mirrors offer a keyhole into questions of the relationships between heaven and earth, body and soul, men and women, and beyond. Rhetoric of vision can divide along lines of gender or baptismal status, or it can envision connection to or distance from God. How we understand vision shapes what and how we see and also our broader senses of self, and to miss how sight worked for late ancient authors, therefore, is to look past some of the most self-conscious ways that late ancient Christians thought of themselves, their worlds, and their God.
Augustine of Hippo
Authors: Cain Emily R.
Published: January 2023

Many have helpfully written about the tension between Augustine’s affirmation of human free will and his seemingly contradictory emphasis on God’s divine grace. This chapter approaches this ostensible paradox not directly, but rather indirectly; that is, not through Augustine’s content on the topic, but rather through his method. An examination of Augustine’s writing on visual perception, particularly that found in his de Trinitate, reveals the way in which he constructs this complicated and paradoxical relationship though vision’s subjectivity, describing a human who is simultaneously active and responsible for harmful actions, yet passive against the resultant transformation; one who sees God poorly when seeing the world poorly; and one who, paradoxically, has free will, yet stands in need of God’s grace. Indeed, it is following his very model of faith seeking understanding that Augustine pulls together outwardly disparate theories of visual perception to describe vision’s subjectivity in his attempt to understand his faith.
Social Welfare Practices in the Premodern Era (c. 1820–1920)
Authors: Dybicz Phillip
Published: January 2023

In Chapter 5 of A Genealogy of the Good and Critique of Hubris, three broad movements in social welfare practices are identified: moral uplift, institutionalization, and environmentalism. Falling within the area of moral uplift are practices such as the Sunday school movement and the charity organization societies. Institutionalization (penitentiaries, insane asylums, almshouses, etc.) represents the government response to addressing social ills. Environmentalism informed such practices as the parks and playgrounds movement, the settlement house movement, and city missions. The transition period to the Modern Discourse is examined with a focus upon how the insights derived from the scientific method were poorly applied. Moral blind spots are seen as social control in the form of cultural imperialism arising from measuring deviance from an ideal standard. Lastly, reflections are offered as to how insights from this period can be applied today by social workers to improve their practice.
The Modern Discourse (c. 1920–Present)
Authors: Dybicz Phillip
Published: January 2023

Chapter 6 of A Genealogy of the Good and Critique of Hubris describes the current Discourse on social welfare: the Modern Discourse. No anecdotes are provided to begin the chapter; rather, three definitions of social work are offered instead. The various elements of the Discourse are then described with periodic references to current practices informed by these definitions to illustrate their alignment with the Discourse. The influence of science heavily informs this Discourse. Marking the beginning of the modern welfare state, the urgent need of this era is identified as maintaining and enhancing the functioning of society. The evolution of individualism within a highly integrated society is described.
Aftermath
Authors: Simpson Thula
Published: January 2023

This chapter discusses the finale of the Second Anglo-Boer (or South African) War (1899-1902), the conflict that pitted the British Empire against the South African Republic and the Orange Free State. It discusses the peacemaking leading to the Treaty of Vereeniging, in which the Boer Republics surrendered their independence. The chapter then considers the post-war reconstruction overseen by Lord Alfred Milner, Britain's High Commissioner for South Africa. This involved him seeking to restore the status quo ante in the agricultural and mining sectors, which required betraying the black African population, many of whom had remained loyal to Britain during the war. It also involved importing Chinese miners, a step that provoked a backlash that transcended the Brit-Boer divide within the white population. That backlash contributed to thwarting Milner's plans for political reconstruction, which centered on "Anglicizing" the white population prior to self-government. The chapter closes with the Natal Rebellion, and Chief Bhambatha's unsuccessful stand against the loss of Zulu independence.
Union and Disunion
Authors: Simpson Thula
Published: January 2023

The increasingly violent opposition between white workers and the Transvaal's political and economic elite, as manifested in the great strikes of 1913 and 1914, opens this chapter. The second Indian passive resistance campaign in 1913 is also discussed, and the weaknesses of Gandhian satyagraha in the South African context are outlined. The chapter also considers the birth of the policy of segregation that would define so much of South African history in the twentieth century. It does so by discussing the politics of the Natives Land Act of 1913, which aimed to territorially partition the country. Also considered is the split in Louis Botha's ruling party as J.B.M. Hertzog broke away to form the Nationalist Party. The chapter considers the SANNC's campaign against the land act. The campaign was interrupted by the outbreak of the Great War. The chapter closes by considering the impact of the commencement of the war on South Africa, including the Afrikaner Rebellion of 1914–15.
Imperial Impi
Authors: Simpson Thula
Published: January 2023

The chapter begins by recounting South Africa's conquest of German South-West Africa, and the split between the pro- and anti-war factions of the (white) Labour movement. The anti-war faction established the International Socialist League (ISL). The chapter follows South African troops on all the major fronts in which they fought, including East Africa, Egypt, Palestine, and the Western Front in Europe. Among the battles discussed are Delville Wood, Marrières Wood, and Square Hill. The South African Native Labour Contingent is also considered, including the tragedy of the SS Mendi disaster. The home front also receives extensive consideration, including the radicalization of the Transvaal SANNC, which owed both to wartime inflation, and the efforts of the ISL. Another aspect of the war at home that receives extensive coverage is the impact of the Spanish Flu of 1918 on South Africa.
Revolt
Authors: Simpson Thula
Published: January 2023

Post-war economic chaos occasioned political ferment in South Africa: the 1920 miners' strike (the first-ever general strike by black South Africans) forms part of this discussion, as does the formation of the Industrial and Commercial Union (ICU) by Clements Kadalie. The chapter also considers the initiatives by the SANNC and the Nationalist Party to lobby the Imperial Government. Their respective appeals for relief from the pass laws and for the restoration of the independence of the Boer republics, were rejected by David Lloyd George. The chapter also discusses the climax of post-war white labor militancy, namely the eruption of the Rand Revolt of 1922. The chapter considers the role of the Communist Party of South Africa (an outgrowth of the ISL), and the early links between South Africans and leaders of the Russian Revolution.
Defiance
Authors: Simpson Thula
Published: January 2023

The Defiance Campaign of 1952 initiated the ANC-led Congress Alliance's efforts at mass action. The effort was fiercely opposed by the government. The government's reaction sparked ANC counter-measures: in response to the state's counter-measures, the ANC in 1953 introduced the M-Plan, a scheme to enable it to continue operating in the event of legal proscription. Nelson Mandela meanwhile encouraged Walter Sisulu to approach Maoist China to inquire about obtaining weapons for a South African armed struggle. The chapter also considers campaigns launched by the Congress Alliance in the mid-1950s, principally those against the Bantu Education Act, the Western Areas removal, and for the Congress of the People. The latter campaign led to the adoption of the Freedom Charter.
States of Emergency
Authors: Simpson Thula
Published: January 2023

This chapter discusses the State of Emergency that followed the Sharpeville Massacre, during which the ANC and PAC were banned, and a revolt in rural Pondoland was crushed by the state. In a referendum, South Africa's Prime Minister, H.F. Verwoerd, obtained white approval to establish a republic, but in the teeth of the hostility of other Commonwealth members, South Africa had to withdraw from that club. Nelson Mandela went underground, organized an abortive strike against the republic, and after that failed, set about obtaining support from his political comrades for an armed struggle. The chapter ends in December 1961 when Umkhonto we Sizwe (of which Mandela was the founding commander), and Poqo, which was an offshoot of the PAC, began military operations. They were joined by a third underground militia, the National Committee of Liberation (NCL).
Total Onslaught
Authors: Simpson Thula
Published: January 2023

Distressed by the slow progress of its armed struggle, the ANC sent a delegation to Vietnam in 1978 to glean the lessons of that country's revolution. The outcome was a new strategy involving armed propaganda to pave the way for people's war. Also considered is the state's implementation of the policy of homeland independence, and why even the participants in that process questioned its credibility. The state also initiated a constitutional reform programme to respond to the growing unrest in the country. The proposals recommended a tricameral Parliament incorporating Asians and coloreds but excluding Africans. These initiatives were accompanied by continuous cross-border military operations to drive the ANC (and SWAPO) from South African controlled borders. The chapter considers the turmoil that the "Total Strategy" occasioned in the Frontline States of southern Africa.
Rainbow Nation
Authors: Simpson Thula
Published: January 2023

The chapter discusses the use of sport for "nation-building" in the immediate post-apartheid years. Among the sporting triumphs of the period were the Rugby World Cup of 1995, the Africa Cup of Nations in 1996, and the medals won in the 1996 Olympic Games. In political terms, the local government elections in 1995 were no less important than the 1994 elections in cementing the ANC's grip on the nation. A major political theme of the time was economic liberalization, and the chapter ends with the increasing controversy within the ANC over macroeconomic policy, whereby advocates of market-friendly approaches were pitted against champions of state-led development.
Reason and Inquiry
Authors: Koralus Philipp
Published: January 2023

This book presents a unified theory of the human capacity for reasoning and decision-making. The erotetic theory accounts for a diverse range of empirically documented fallacies and framing effects and shows how the same mental processes that yield fallacies can yield what logicians call first-order validity and probabilistic coherence in reasoning, as well as rational decision-making as conceived by economists. The central idea is that our minds naturally aim at resolving issues, and if we are sufficiently inquisitive in the process, we can avoid mistakes. The erotetic theory holds that both the successes and the failures of reason are due to this aim. Rationality is secured if we reach what will be called erotetic equilibrium.
Introduction
Authors: Walsham Alexandra
Published: January 2023

This chapter provides the intellectual and historiographical framework for the book. It explores the fertile concept of generation and its multiple and overlapping meanings in the early modern period. It surveys recent scholarship on the English Reformations and evaluates previous attempts to utilize the model of generation as a tool for exploring historical change, which have primarily focused on the modern era. It explains the methodological assumptions that underpin the study. Underlining the value of a generational approach to understanding the successive phases of religious change that marked the sixteenth and seventeenth centuries, it contends that this offers a revealing new lens onto the theological, liturgical, and cultural upheavals of the period. It also introduces the rich and varied body of source material on which the core chapters are based, summarizes the book’s architecture and structure, and highlights its principal arguments.
Generations and Seed
Authors: Walsham Alexandra
Published: January 2023

This chapter argues that consciousness of being part of a historical or chosen generation was one of the by-products of the English Reformations. It examines the implications of the biblical language of generations and seed in early modern thinking and investigates what this reveals about senses of group identity derived from a shared location in time. It explores the various ways in which religious change engendered senses of belonging to a particular cohort bound by common experiences and transformed how people understood their relationships with their ancestors and descendants. It demonstrates that generational awareness was a mode of subjectivity intimately connected with the workings of memory, but that it also gave expression to collective hopes and dreams about the future, especially in the mid-seventeenth century, when the concept of ‘generation work’ became prominent in contemporary discourse. The chapter also examines the pressing questions that devout people from all denominations faced about the spiritual fate of their dead relatives and about how to ensure the salvation of their children and heirs. It traces these dilemmas and debates across the Atlantic to New England, where the appealing notion that election was in some sense a birthright found expression in the Half-Way Covenant.
Social Context and Legal Developments
Authors: Fredman FBA KC Sandra
Published: January 2023

This chapter examines the evolution of the right to equality in relation to sexual orientation, gender identity, disability, and age in the UK (including the EU and ECHR), US, Canada, India, and South Africa, demonstrating the ways in which anti-discrimination law responds to the social and historical context in which it is embedded. For all of these, a key first step has been to acknowledge the role of society in obscuring these identities and to recognize and conceptualize the rights-bearers as full participants in society. Equality laws must then be shaped to further the right to equality on all four dimensions of substantive equality.
The Insanity Defence in French Law
Authors: Guinchard Audrey
Published: January 2023

In 2016, the Human Rights Watch report on French prisons concluded that the mentally ill offenders suffer ‘a double punishment’, as they are likely to be sentenced to prison for longer and with inadequate care. One identified factor was Article 122-1 of the Criminal Code (CP), which defines the French ‘insanity’ defence. Using a historical perspective and contemporary medico-legal writings, this chapter demonstrates that the 1992 re-codification of the French law defence of mental disorder in Article 122-1 CP has exposed and accentuated perennial fault lines in the articulation of the defence’s important features: the definition of the disorder to trigger the defence; the understanding of the impact the disorder should have for the defence to be accepted; and the modulation of the outcome of the defence in light of prior fault. Determining the boundaries between responsibility, irresponsibility, and attenuated responsibility has never been as straightforward as is often claimed. The fraught and tense debates which have surrounded the case of Halimi, decided in April 2021 by the French Supreme Court, confirm the need for clarification and reform. This evolution of the French law defence in turn sheds light on English criminal law’s own approach to the insanity defence and its satellites: automatism, diminished responsibility, and intoxication.
Criminal Insanity in Norwegian Law
Authors: Gröning Linda
Published: January 2023

This chapter will discuss the current Norwegian rules concerning criminal incapacity and insanity as defined in section 20 of the Norwegian Penal Code, considered from both historical and comparative perspectives. These rules came into force on 1 October 2020, as the result of the law reform that was initiated in the aftermath of the case concerning Anders Behring Breivik, who killed 77 people in Oslo and at Utøya on 22 July 2011. The chapter also includes an overview of the central approaches and systems in Norwegian insanity law and a discussion about the background of the current rules and the law reform in 2020.
The Insanity Defence in China
Authors: Jiang Lilou
Published: January 2023

This chapter critically examines the insanity defence regime in China. It presents the evolution of the criteria and procedures surrounding the insanity defence, depicts the decisive role that psychiatric assessment plays in the proceedings, and then investigates the factors militating against China’s judicial authority from ordering a psychiatric assessment for capital crime offenders raising the defence of insanity. As will be observed, the procedural and evidentiary rules for raising the insanity defence in China are radically different from western countries. It further examines the public stigma in Chinese society and traditional philosophical thoughts behind the historical harsh treatment of mentally ill offenders. Finally, it concludes that the insanity defence has not effectively exempted capital crime offenders with mental illness from the death penalty, and the punitive attitude towards mental illness will continue influencing stakeholders’ choices in the context as long as China’s judicial system emphasizes the superiority of social stability over individual human rights.
Conclusion
Authors: Mackay Ronnie , Brookbanks Warren
Published: January 2023

This chapter offers a brief survey on various formulations and reformulations of the insanity defence as reflected in both common law and civil law jurisdictions. Throughout this discussion the significance of the role of the Convention on the Rights of Persons with Disabilities is acknowledged and its potential impact on future formulations of the insanity defence, pointing towards the continued need for reform. The chapter contains a brief commentary on the principal elements of each chapter and offers some final thoughts on how the varied jurisdictions which are the subject of this volume reveal some fundamental commonalities and constant aspects, in particular the continued favouring of M’Naghten Rules based defences in a number of common law jurisdictions.
Synthesis
Authors: Schobert Harold
Published: January 2023

The mixture of carbon monoxide and hydrogen produced from gasification is an extraordinarily versatile material. It can be used directly as a fuel, but also used as a raw material to produce a variety of other gaseous and liquid fuels, as well as chemical products. The CO–H2 mixture is called synthesis gas. The composition of the synthesis gas can be adjusted to any desired value via the water–gas shift reaction. Subsequent uses of the “shifted” gas include formation of synthetic gasoline and other liquid fuels; substitute natural gas; and methanol, useful as a fuel itself, for production of chemicals, or for conversion to gasoline. Synthesis gas technology is tremendously versatile, offering a route from coal (or other carbon sources) to liquid fuels, gaseous fuels, and many products used in the chemical industry. However, this technology has prodigious emissions of carbon dioxide and a significant appetite for water.
Vector bundles on fuzzy Kähler manifolds
Authors: Adachi Hiroyuki , Ishiki Goro , Kanno Satoshi
Published: January 2023

We propose a matrix regularization of vector bundles over a general closed Kähler manifold. This matrix regularization is given as a natural generalization of the Berezin–Toeplitz quantization and gives a map from sections of a vector bundle to matrices. We examine the asymptotic behaviors of the map in the large-N limit. For vector bundles with algebraic structure, we derive a beautiful correspondence of the algebra of sections and the algebra of corresponding matrices in the large-N limit. We give two explicit examples for monopole bundles over a complex projective space CPn and a torus T2n.
Interventional Radiology Management of Vascular Complications From Gastrointestinal Interventions
Authors: Narayanan Harish A. , Naidu Sailendra G. , Alzubaidi Sadeer , Patel Indravadan , Staack Sasha , Oklu Rahmi
Published: January 2023

Recent advances in gastrointestinal interventions have led to the development of percutaneous and endoscopic procedures that can be performed in minimally invasive manner as an alternate to invasive surgery. Although the vast majority of these procedures have successful outcomes, there are potential complications. The diagnosis of these complications is often elusive. Interventional radiology can offer minimally invasive management of such complications. This educational activity aims to illustrate this through a review of several cases encountered at our institution.
Prevalence of at-risk NASH and its association with metabolic syndrome in US adults with NAFLD, 2017–2018
Authors: Payne Julia Y. , Alkhouri Naim , Le Phuc , Rothberg Michael B. , Polanco Prido , Sakkal Celine , Dasarathy Srinivasan
Published: January 2023

Patients with metabolic syndrome (MetS) have a higher risk for NASH and significant fibrosis. Presence of NASH and advanced fibrosis are associated with adverse outcomes in patients with NAFLD. Using a noninvasive method, we determined the prevalence of at-risk NASH and its association with MetS components in a large population-based analysis. We used the 2017–2018 National Health and Nutrition Examination Survey and included adults ≥18 years with NAFLD (controlled attenuation parameter ≥274 dB/m). Pregnancy, subjects with other causes of liver disease or missing data were excluded. FibroScan-AST (FAST) score was calculated using aspartate aminotransferase, liver stiffness measurement, and controlled attenuation parameter. Patients with a FAST score >0.35 were considered to have at-risk NASH, defined as NASH with NAFLD activity score ≥4 and fibrosis stage ≥2 on liver biopsy. The sample included 687 patients. The overall prevalence of at-risk NASH was 11.6% (95% CI: 8.8–15.1) and was higher in males than females (15.8% vs. 6.5%; p < 0.001). Subjects with comorbidities (diabetes mellitus, obesity, MetS, and insulin resistance) had between 1.3 and 1.7 times higher prevalence than the general population. Among MetS components, elevated glucose/diabetes, large waist circumference, and low HDL were independent risk factors for at risk-NASH. The number of MetS components was also important—one additional component increased the odds of at-risk NASH by 2 times. The FAST score had the highest correlation with alanine aminotransferase (r= 0.70; p < 0.001). We estimated ~9 million people in the US have at-risk NASH and may benefit from active surveillance and therapy.
Piggybacking on Danger: The Link Between Swine and Hepatitis E Virus
Authors: Yodjan Naluepanat
Published: January 2023

The hepatitis E virus (HEV) is a significant public health concern worldwide and has been associated with the consumption of contaminated pork products and occupational exposure to infected swine. Swine can act as a reservoir of HEV for humans, and the epidemiology of HEV in swine populations is complex and varies depending on the region and population. This article reviews the current knowledge on the link between swine and HEV, including the epidemiology, transmission dynamics, and public health implications of HEV in swine. The article also discusses the current prevention and control measures that have been implemented to reduce the risk of HEV infection in humans and to control HEV epidemiology. The article also highlights the importance of the One Health approach and future research directions that are needed to understand better the epidemiology and transmission dynamics of HEV in swine populations and to develop effective control measures to reduce the burden of HEV infections worldwide.
Unveiling abundance-dependent metabolic phenotypes of microbial communities
Authors: Jiménez Natalia E. , Acuña Vicente , Cortés María Paz , Eveillard Damien , Maass Alejandro
Published: January 2023

Constraint-based modeling has risen as an alternative for characterizing the metabolism of communities. Adaptations of Flux Balance Analysis have been proposed to model metabolic interactions in most cases, considering a unique optimal flux distribution derived from the maximization of biomass production. However, these approaches do not consider the development of other potentially novel essential functions not directly related to cell growth which forces them to display suboptimal growth rates in nature. Additionally, suboptimal states allow a degree ofplasticityin the metabolism, thus allowing quick shifts between alternative flux distributions as an initial response to environmental changes.

In this work, we present a method to explore theabundance-growth spaceas a representation of metabolic flux distributions of a community. This space is defined by the composition of a community, represented by its members’ relative abundance and their growth rate. The analysis of this space allows us to represent the whole set of feasible fluxes without needing a complete description of the solution space unveiling abundance-dependent metabolic phenotypes displayed in a given environment. As an illustration, we consider a community composed of two bioleaching bacteria,Acidithiobacillus ferrooxidansWenelen andSulfobacillus thermosulfidooxidansCutipay, finding that changes in the composition of their available resources significantly affects their metabolic plasticity.

IMPORTANCE

In nature, organisms live in communities and not as isolated species. Their interactions provide a source of resilience to environmental disturbances. Despite their importance in ecology, human health, and industry, understanding how organisms interact in different environments remains an open question.

In this work, we provide a novel approach which, only using genomics information, studies the metabolic phenotype exhibited by communities, where the exploration of suboptimal growth flux distributions and the composition of a community allows to unveil its capacity to respond to environmental changes, shedding the light of the degree of metabolic plasticity inherent to the community.
A Novel Algorithm to Calculate Elementary Modes: Analysis ofCampylobacter jejuniMetabolism
Authors: Said Yanica , Singh Dipali , Sebu Cristiana , Poolman Mark
Published: January 2023

We describe a novel algorithm, ‘LPEM’, that given a steady-state flux vector from a (possibly genome-scale) metabolic model, decomposes that vector into a set of weighted elementary modes such that the sum of these elementary modes is equal to the original flux vector.

We apply the algorithm to a genome scale metabolic model of the human pathogenCampylobacter jejuni. This organism is unusual in that it has an absolute growth requirement for oxygen, despite being able to operate the electron transport chain anaerobically.

We conclude that 1) Microaerophilly inC. jejunican be explained by the dependence of pyridoxine 5′ -phosphate oxidase for the synthesis of pyridoxal 5′ - phosphate (the biologically active form of vitamin B6), 2) The LPEM algorithm is capable of determining the elementary modes of a linear programming solution describing the simultaneous production of 51 biomass precursors, 3) Elementary modes for the production of individual biomass precursors are significantly more complex when all others are produced simultaneously than those for the same product in isolation and 4) The sum of elementary modes for the production of all precursors in isolation requires a greater number of reactions and overall total flux than the simultaneous production of all precursors.
Systemic orchestration of cell size throughout the body: Influence of sex and rapamycin exposure inDrosophila melanogaster
Authors: Szlachcic Ewa , Labecka Anna Maria , Privalova Valeriya , Sikorska Anna , Czarnoleski Marcin
Published: January 2023

Along with differences in life histories, metazoans have evolved vast differences in cellularity, involving changes in the molecular pathways controlling the cell cycle. The extent to which the signalling network systemically determines cellular composition throughout the body and whether tissue cellularity is organized locally to match tissue-specific functions are unclear. We cultured genetic lines ofDrosophila melanogasteron food with and without rapamycin to manipulate the activity of TOR/insulin pathways and evaluate cell-size changes in five types of adult cells: wing and leg epidermal cells, ommatidial cells, indirect flight muscle cells, and Malpighian tubule epithelial cells. Rapamycin blocks TOR multiprotein complex 1, reducing cell growth, but this effect has been studied in single cell types. As adults, rapamycin-treated flies had smaller bodies and consistently smaller cells in all tissues. Regardless, females eclosed with larger bodies and larger cells in all tissues than males. Thus, differences in TOR activity and sex were associated with the orchestration of cell size throughout the body, leading to differences in body size. We postulate that the activity of TOR/insulin pathways and their effects on cellularity should be considered when investigating the origin of ecological and evolutionary patterns in life histories.
Canary in the Forest? – Tree mortality and canopy dieback of western redcedar linked to drier and warmer summer conditions
Authors: Andrus R.A. , Peach L.R. , Cinquini A.R. , Mills B. , Yusi J.T. , Buhl C. , Fischer M. , Goodrich B.A. , Hulbert J.M. , Holz A. , Meddens A.J.H. , Moffett K.B. , Ramirez A. , Adams H.D.
Published: January 2023

Tree mortality and partial canopy dieback are increasing in many forest ecosystems from unfavorable climate conditions. Examining how tree growth and mortality are affected by climate variability can help identify proximate causes of tree mortality and canopy dieback. We investigated anomalously high mortality rates and partial canopy dieback of western redcedar (Thuja plicata, WRC), a culturally, ecologically, and economically important species in the Pacific Northwest (USA), using tree-ring methods. We sampled trees in three tree status groups—no canopy dieback, partial canopy dieback, and trees that died (0-30 years ago)—from 11 sites in coastal (maritime climate) and interior (continental climate) populations of WRC trees. In our study, WRC tree mortality was portended by on average 4-5 years of declining radial growth. Warmer and drier climate conditions in May and June that extend the annual July-September dry season reduced radial growth in 9 of 11 sites (1975-2020). Defining drought events as warm, dry May-June climate, we found that WRC trees recovered radial growth to pre-drought rates within three years when post-drought climate conditions were average or cooler and wetter than average. However, radial growth recovery from drought was slower or absent when conditions were warmer and drier during the post-drought recovery period, which appeared to lead to the widespread mortality event across coastal populations. Annually resolved tree mortality in coastal populations predominately occurred in 2017-2018 (80% of sampled trees) and coincided with exceedingly hot temperatures and the longest regionally dry period for May to September (1970-2020). In interior populations, tree mortality was associated with warmer, drier conditions from August to September. Our findings forewarn that a warming climate and more frequent and severe seasonal droughts will likely increase the vulnerability of WRC to canopy dieback and mortality and possibly other drought-sensitive trees in one of the world’s largest carbon sinks.
Sensitive inference of alignment-safe intervals from biodiverse protein sequence clusters using EMERALD
Authors: Grigorjew Andreas , Gynter Artur , Dias Fernando H. C. , Buchfink Benjamin , Drost Hajk-Georg , Tomescu Alexandru I.
Published: January 2023

Sequence alignments are the foundation of life science research, but most innovation focused on optimal alignments, while ignoring information derived from suboptimal solutions. We argue that one optimal alignment per pairwise sequence comparison was a reasonable approximation when dealing with very similar sequences, but is insufficient when exploring the biodiversity of the protein universe at tree-of-life scale. To overcome this limitation, we introduce pairwise alignment-safety to uncover the amino acid positions robustly shared across all suboptimal solutions. We implemented this approach into EMERALD, a dedicated software solution for alignment-safety inference and apply it to 400k sequences from the SwissProt database.
Variational graph encoders: a surprisingly effective generalist algorithm for holistic computer-aided drug design
Authors: Lam Yuen In Hilbert , Pincket Robbe , Han Hao , Ong Xing Er , Wang Zechen , Li Weifeng , Hinks Jamie , Zheng Liangzhen , Wei Yanjie , Mu Yuguang
Published: January 2023

1.

While there has been significant progress in molecular property prediction in computer-aided drug design, there is a critical need to have fast and accurate models. Many of the currently available methods are mostly specialists in predicting specific properties, leading to the use of many models side-by-side that lead to impossibly high computational overheads for the common researcher. Henceforth, the authors propose a single, generalist unified model exploiting graph convolutional variational encoders that can simultaneously predict multiple properties such as absorption, distribution, metabolism, excretion and toxicity (ADMET), target-specific docking score prediction and drug-drug interactions. Considerably, the use of this method allows for state-of-the-art virtual screening with an acceleration advantage of up to two orders of magnitude. The minimisation of a graph variational encoder’s latent space also allows for accelerated development of specific drugs for targets with Pareto optimality principles considered, and has the added advantage of explainability.
Structural Interaction Fingerprints and Machine Learning for predicting and explaining binding of small molecule ligands to RNA
Authors: Szulc Natalia A. , Mackiewicz Zuzanna , Bujnicki Janusz M. , Stefaniak Filip
Published: January 2023

Ribonucleic acids (RNA) play crucial roles in living organisms as they are involved in key processes necessary for proper cell functioning. Some RNA molecules, such as bacterial ribosomes and precursor messenger RNA, are targets of small molecule drugs, while others, e.g., bacterial riboswitches or viral RNA motifs are considered as potential therapeutic targets. Thus, the continuous discovery of new functional RNA increases the demand for developing compounds targeting them and for methods for analyzing RNA—small molecule interactions. We recently developed fingeRNAt - a software for detecting non-covalent bonds formed within complexes of nucleic acids with different types of ligands. The program detects several non-covalent interactions, such as hydrogen and halogen bonds, ionic, Pi, inorganic ion-and water-mediated, lipophilic interactions, and encodes them as computational-friendly Structural Interaction Fingerprint (SIFt). Here we present the application of SIFts accompanied by machine learning methods for binding prediction of small molecules to RNA targets. We show that SIFt-based models outperform the classic, general-purpose scoring functions in virtual screening. We discuss the aid offered by Explainable Artificial Intelligence in the analysis of the binding prediction models, elucidating the decision-making process, and deciphering molecular recognition processes.

Key Points

Structural Interaction fingerprints (SIFts), combined with machine learning, were successfully used to develop activity models for ligands binding to RNA.

SIFt-based models outperformed the classic, general-purpose scoring functions in virtual screening.

Explainable Artificial Intelligence allowed us to understand the decision-making process and decipher molecular recognition processes in the analysis of RNA—ligand binding activity models.

We provide a benchmark dataset based on ligands with known or putative binding activity toward six RNA targets. It can be readily used by the scientific community to test new algorithms of virtual screening on RNA—ligand complexes.
Description ofProtosticta armageddonensis sp. nov. (Odonata: Zygoptera: Platystictidae) from the Western Ghats of India
Authors: Payra Arajush , Chandran Reji , Deshpande Ameya , Koparde Pankaj
Published: January 2023

A new species ofProtostictaSelys, 1885 (Odonata: Zygoptera: Platystictidae) is described based on two male specimens collected from Kerala, at the southern end of the Western Ghats in India. We comparedP. armageddonensissp. nov. with the three closely similarProtostictaspecies recently described from the Western Ghats, namelyP.anamalaicaSadasivan, Nair & Samuel, 2022,P. cyanofemoraJoshi, Subramanian, Babu & Kunte, 2020, andP. monticolaEmiliyamma & Palot, 2016, to provide comprehensive differential diagnosis. The new species is distinguished from its congeners by a combination of characters, including the structure of prothorax, caudal appendages, genital ligula, and markings on the 8th abdominal segment. A revised key ofProtostictaspp. of the Western Ghats, based on mature male specimens is provided.
Phosphorylation of PSD-95 at Serine 73 in dCA1 is required for extinction of contextual fear
Authors: Ziółkowska Magdalena , Borczyk Malgorzata , Cały Anna , Nalberczak-Skóra Maria , Nowacka Agata , Śliwińska Małgorzata Alicja , Łukasiewicz Kacper , Skonieczna Edyta , Tomaszewski Kamil F. , Wójtowicz Tomasz , Włodarczyk Jakub , Bernaś Tytus , Salamian Ahmad , Radwanska Kasia
Published: January 2023

The updating of contextual memories is essential for survival in a changing environment. Accumulating data indicate that the dorsal CA1 area (dCA1) contributes to this process. However, the cellular and molecular mechanisms of contextual fear memory updating remain poorly understood. Postsynaptic density protein 95 (PSD-95) regulates the structure and function of glutamatergic synapses. Here, using dCA1-targeted genetic manipulationsin vivo, combined withex vivo3D electron microscopy and electrophysiology, we identify a novel, synaptic mechanism that is induced during attenuation of contextual fear memories and involves phosphorylation of PSD-95 at Serine 73 in dCA1. Our data provide the proof that PSD-95-dependent synaptic plasticity in dCA1 is required for updating of contextual fear memory.
Oviposition behaviour is not affected by ultraviolet light in a butterfly with sexually-dimorphic expression of a UV-sensitive opsin
Authors: Malo Jose Borrero , Wright Daniel Shane , Bacquet Caroline Nicole , Merrill Richard M.
Published: January 2023

Animal vision is important for mediating multiple complex behaviours. InHeliconiusbutterflies, vision guides fundamental behaviours such as oviposition, foraging and mate choice. Colour vision inHeliconiusinvolves ultraviolet (UV), blue and long-wavelength sensitive photoreceptors (opsins). Additionally,Heliconiuspossess a duplicated UV opsin, and its expression varies widely within the genus. InHeliconius erato, opsin expression is sexually dimorphic; only females express both UV-sensitive opsins, enabling UV wavelength discrimination. However, the ecological pressures that have driven these sex-specific differences in visual perception remain unresolved.Heliconiusfemales invest heavily in finding hostplants to lay their eggs, a behaviour heavily reliant on visual cues. We tested whether UV vision is used for oviposition inH. eratoandHeliconius himerafemales by manipulating the availability of UV in behavioural experiments under naturalistic conditions. We found that UV did not influence the number of oviposition attempts or the number of eggs laid. In addition, their hostplant,Passiflora punctata, does not reflect UV wavelengths, and models ofH. eratofemale vision suggest only minimal stimulation of the UV opsins. Overall, these findings suggest that UV wavelengths do not directly affect the ability ofHeliconiusfemales to find suitable oviposition sites. Alternatively, UV discrimination could be used in the context of foraging or mate choice, but this remains to be tested.