bluuebunny/crossref_metadata_2025 huggingface dataset:
Pensions and ESG
Authors: Hammond P. Brett , O’Brien Amy
Published: July 2023

Sustainable investing is growing into its moment. Funded pensions, which were among the first institutions to respond to sustainability concerns, are showing renewed interest in better ways to reflect responsible investing objectives, along with regulators, asset managers, and shareholder groups. Looking back, the principal elements of sustainability—environmental, social, and governance (ESG)—all have different origins and have taken different pathways. Looking across the world, sustainable investing developed differently depending on region and country. Viewing it today, we see the trend toward E, S, and G convergence—of definition, process, and organization—toward a more integrated investment perspective and process. With growing asset size, funded pensions, sovereign wealth funds, and other large institutional investors became ‘universal owners’ and, along with thought leaders and regulators, drove the evolution of sustainable investing toward the more systematic set of tools and policies we see today. Looking forward, questions remain, such as who will be most influential in determining the future of sustainable investing—pensions and other institutional investors, governments, shareholders, or companies—as well as what it will look like. As such, sustainability remains a work in progress and pensions are in a strong position to shape its evolution.
Institutional Controls and Autocratic Survival
Authors: Duvanova Dinissa
Published: July 2023

Reflecting on the notion that clear and detailed regulations can discipline the public bureaucracy and positively affect the business climate, this chapter examines constraints and opportunities for building sound regulatory states by the autocratic regimes. It scrutinizes the empirical implications of the logic of the autocrat's dilemma in promoting public or elite interests. I hypothesize that in times when considerations of political survival make politicians prioritize national economic performance over elite enrichment, discretionary policy implementation is likely to be scaled back with the adoption of detailed statutory, executive, or agency-level regulations. The large-N quantitative data analysis reveals that accelerated development of discretion-constraining regulatory detail generally follows periods of declining oil rents, and at the regional level in Russia, periods of heightened protest activities. Moreover, at the regional level in Russia, mass protests that signal rising popular grievances reinvigorate regional discretion-constraining rulemaking.
The ATR/Laryngeal connection and emergent features
Authors: Iosad Pavel
Published: July 2023

‘Substance-free’ theories of phonology take two different approaches to eliminating phonetic information from phonological computations, positing either that distinctive features have phonetic content but phonological rules can manipulate them in arbitrary ways (Hale & Reiss 2003, 2008) or that features are based on phonological patterning and need not have any identifiable phonetic content at all (Blaho 2008; Samuels 2009). This chapter argues that the key insights of substance-free phonology can be maintained in a system that allows a limited role for phonetic substance. Methodologically, requiring that features have phonetic content and rules be formally natural limits the generative power of the system, forcing analysts to look more closely at apparently unnatural rules and classes, and precluding analyses based on spurious generalizations. At the same time, the fact that phonetic content does not always determine phonological patterning can be explained through underspecification based on contrast.
The Philosophy Curriculum at Scottish Universities in the Eighteenth Century
Authors: Ahnert Thomas
Published: July 2023

This chapter examines the changes in the main parts of the university curriculum in philosophy—logic, rhetoric, metaphysics, pneumatics, natural philosophy, and ethics—in the period from c.1690 to c.1830. Underlying developments in these various philosophical subdisciplines was a rejection of ‘speculative philosophy’ in favour of a ‘culture of the mind’. ‘Speculative philosophy’ had, on the whole, been a value-free term at the beginning of the century, when it was part of a division of philosophy into ‘speculative’ and ‘practical’ branches. But from the first decades of the eighteenth century, ‘speculation’ was increasingly associated with the corruption of philosophy by the abstruse and futile intellectual quarrels of so-called ‘scholastics’. By the end of the century, the former distinction between ‘speculative’ and ‘practical’ branches of philosophy had been replaced by an alternative division of philosophy into the study of mind and the study of matter.
Theories of Perception
Authors: Grandi Giovanni B.
Published: July 2023

This chapter discusses the views on sensory perception of four authors: William Porterfield, Thomas Reid, Dugald Stewart, and Adam Smith. In eighteenth-century Scotland theories of perception were developed by both philosophers and physiologists. Special attention was paid to the role that innate mechanisms and experience play in the workings of our senses. Although various phenomena of sensory perception were discussed, the appearance of Berkeley’s Essay towards a New Theory of Vision (1709) led to a particular emphasis on sight and its relation to touch. Writers on perception were not only interested in questions strictly pertaining to the psychology of vision, but also reacted to Berkeley’s immaterialism and to Hume’s scepticism.
Habit and the Association of Ideas in the Scottish Enlightenment
Authors: Wright John P. , Tabb Kathryn
Published: July 2023

This chapter examines discussions of association of ideas and habit pursued by philosophers of the Scottish Enlightenment. It is argued that they played a fundamental role not only in epistemology, but also in aesthetics and morality. Beginning with Hutcheson’s adoption of Locke’s treatment of association as the basis for pathological beliefs the chapter proceeds to the positive accounts of its role in reasoning and action presented by Hume and Turnbull. As well as expanding the principles of association of ideas beyond those formed by habit, Hume left questions about the relationship of association and habit which were explicitly dealt with by his successors. The chapter explores the further expansion of the principles of association by Kames, Gerard, Reid, and Stewart, as well as the debates about whether association or habit was a more basic principle of human nature. In the conclusion, the authors note the changes in the treatment of these topics in the nineteenth century.
Island environments
Authors: Whittaker Robert J. , Fernández-Palacios José María , Matthews Thomas J.
Published: July 2023

‘Island environments’ examines variation in environmental properties of islands, highlighting the range of distinctive classes of island in terms of geology, topography, and climate, and how they contrast with mainland environments. It discusses edaphic properties linked to their distinctive geological origins, noting the importance of marine and atmospheric subsidies to their nutrient cycles. It describes island climate regimes and climate zonation compression on high islands and shows that island position in relation to large-scale features of the climate, marine and atmospheric currents, and hurricane systems, are all key features of island environments. It highlights the importance of continued volcanism and mega-landslides for many islands. It describes how Quaternary climate change has impacted island environments both directly and through fluctuations in sea level, sometimes to slightly higher and for lengthy periods much lower levels than present. Finally, it briefly introduces the theme of anthropogenic environmental change on islands.
Island macroecology
Authors: Whittaker Robert J. , Fernández-Palacios José María , Matthews Thomas J.
Published: July 2023

‘Island macroecology’ reviews the emergent statistical properties of island biotas. It depicts MacArthur and Wilson’s 1967 equilibrium theory of island biogeography, describing how area and isolation control rates of immigration, extinction, and cladogenesis. It applies these ideas to understanding of island species–area relationships (ISARs). ISAR form is reviewed, highlighting a range of models of varying complexity, but concluding that the power model remains the best general model of ISAR form. ISAR power model parameters and fits are shown to vary in relation to archipelago configuration, climate, and environmental properties, and to biological properties such as chorotype and taxon. Rarity of island species is described via variation in the species abundance distribution and range size/occupancy relationships. Turnover of species is assessed in relation to sources of error, relationships with island characteristics, and natural extinction drivers. It concludes with a review of evidence for dynamic equilibrium at island and archipelago levels.
Assembly rules for island metacommunities
Authors: Whittaker Robert J. , Fernández-Palacios José María , Matthews Thomas J.
Published: July 2023

‘Assembly rules for island metacommunities’ reviews the search for hidden tramlines in the composition of island biotas (i.e. non-random patterns that may carry biological meaning). It highlights three general challenges: the detection, attribution, and resolution problems. It describes Jared Diamond’s seminal studies of incidence functions, checkerboards, and related distributional patterns for Bismarck Island land birds. It reviews subsequent literature exploring the distinction between analyses restricted to ecological guilds and to broader groups or metacommunities and the roles of trophic hierarchies and of ecological networks. It reviews species incidence functions, nested distributions (where island biotas are proper subsets of successively richer islands), and beta diversity partitioning, each reflecting insular species’ responses to island properties. It describes functional and phylogenetic diversity metrics and their application to island biotas. It reviews longitudinal studies of island disassembly following disruption, and of island assembly, principally through data for Surtsey and the Krakatau Islands.
Colonization, evolutionary change, and speciation
Authors: Whittaker Robert J. , Fernández-Palacios José María , Matthews Thomas J.
Published: July 2023

‘Colonization, evolutionary change, and speciation’ considers how founder populations may develop into island endemic forms. It briefly reviews the nature of the species unit, where species and subspecies fit into the taxonomic hierarchy, and the use of molecular methods, stem age, and crown age, in the depiction and dating of evolutionary relationships. It notes the distinctions between allopatry, sympatry, and parapatry in island evolution, and between novelty arising within islands and endemism through relictualism. It describes and evaluates, using case-study evidence, the phenomena of founder effects, genetic bottlenecks and genetic drift, natural selection and sexual selection, alongside processes of ecological release, density compensation, and character displacement. It describes general speciation models under the frameworks of allopatric/geographical speciation, competitive speciation, and hybridization, noting the imperfectly understood links between hybridization, polyploidy, and apomixis. It concludes with a brief evaluation of anagenesis and cladogenesis as frameworks for insular analysis.
Evolutionary diversification across islands and archipelagos
Authors: Whittaker Robert J. , Fernández-Palacios José María , Matthews Thomas J.
Published: July 2023

‘Evolutionary diversification across islands and archipelagos’ identifies, outlines, and evaluates three general models: the taxon cycle, adaptive radiation, and non-adaptive radiation, each in an insular context. It evaluates taxon cycles through case studies on Melanesian ants, and birds from the Caribbean, Hawaii, and Melanesia. It examines adaptive radiation, illustrated through multiple oceanic island systems and fish radiations in lakes, noting the roles of trait disparification and convergence. It considers whether adaptive radiation is a race towards specialization. Non-adaptive radiation is illustrated through insular snails. Detailed attention is given to Hawaiian lobeliads and Macaronesian Laparocerus weevils, demonstrating the fine-scale relationships between island geodynamics and the most impressive radiations. It describes and evaluates the island progression rule, back colonization, and upstream island–mainland colonization events and their prevalence for selected case-study systems. It draws upon consideration of in situ and external biotic and environmental drivers and mechanisms of insular evolutionary change.
The human transformation of island ecosystems
Authors: Whittaker Robert J. , Fernández-Palacios José María , Matthews Thomas J.
Published: July 2023

‘The human transformation of island ecosystems’ documents the timing and impact of the human colonization of the world’s islands. It distinguishes between palaeoinhabited islands (settled > 2 ka), neoinhabited islands, and those first colonized during the European age of expansion (15th century onwards). It describes the great range in initial contact and settlement dates within each major ocean basin. It describes the concept of a prehistoric island survival kit, the package of commensals, and practices underpinning multiple successful colonization events. It notes that modern European colonization frequently induced dramatic changes to earlier island peoples and societies as well as to island environments and biotas, although prehistoric settlement was also typically impactful. It provides accounts for the Caribbean, Micronesia, Macaronesia, and Polynesia (e.g. Rapa Nui/Easter Island), demonstrating subtle differences in the transformation and biotic homogenization of islands brought about by the different cultural waves that have swept over the world’s islands.
Conclusion
Authors: Forjwuor Bernard
Published: July 2023

The concluding chapter summarizes the key points in this book. The emphasis of this summary is to highlight the evolution of the colonial in present postcolonial politics. The persistence of the colonial, the chapter argues, is sustained through, and because of, normative epistemological traditions that foreclose engagement of the colonial in its complexity. Thus, it argues that normative political theory must be transcended because of the ways it totalizes and demarcates the plane of politics in Africa as affirmation of Eurocentrism. By this objection to normativity, the author is not suggesting at the same time that we abandon any further discussion of colonialism and Eurocentrism. Instead, he strongly suggests we abandon reinscribing normativity/Eurocentrism as innovation and move beyond the enlightenment as critique.
In Defence of the National Interest
Authors: Kinsey Christopher
Published: July 2023

This chapter examines the use of mercenaries in Yemen by the UK and Saudi governments. What it highlights is UK government hypocrisy towards the use of mercenaries, but also the extent it went to hide its involvement while benefiting politically and strategically from their actions. Mercenaries offered the British government a robust and covert option to protect its interests in the Federation of South Arabia. However, the operation also came with considerable political risk if discovered and would certainly have been seen as very controversial in the eyes of the international community if exposed, but more so given the UK government’s objection to the use of mercenaries in the Congo. The other critical aspect of the operation was the role of the Crown Prince of Saudi Arabia in supporting the mercenaries. As the chapter points out, it was Saudi Arabia and not the UK that benefited the most from their actions. This was due to the Crown Prince being able to better manage the competing logics that shaped his decisions. Not only was he able to successfully deny having anything to do with the mercenaries by operating through proxies, he was also able to control their actions through financing and supplying their operation. This last point is important as it enabled him to achieve politically what he needed to, and then close the operation down.
Mercenaries and Private Military and Security Companies as State Instruments of Foreign Security Assistance
Authors: Kinsey Christopher
Published: July 2023

This chapter covers the USA, Russia, and China and their use of mercenaries/private military contractors in Africa to support their foreign policy objectives. The use of mercenaries and military contractors enables government to circumvent sociopolitical constraints attached to the mobilization on uniformed personnel. These constraints include domestic aversion to high casualties, and political scrutiny by domestic opponents. What is more, these constraints appear to be similar, if not the same, faced by all three states. However, unlike the Cold War, the use of mercenaries/private military contractors is not shrouded in secrecy. Ultimately, the use of private force offers political leaders a way to connect the gap between governments’ national security objectives and domestic political constraints over the conduct of foreign policy. The chapter also seeks to explain each country’s different approach to using mercenaries/military contractors on the continent. This is particularly the case regarding Russia and China. Russia has very limited resources to engage in open competition with the West in Africa, such as in providing foreign military assistance programmes. Therefore, it has chosen to turn to Russian private military contractors as a way of negotiating both domestic political constraints and material shortfalls. China, on the other hand, has yet to rely on private military contractors, However, it has used private security companies, while this reliance is likely to increase as China’s presence in Africa grows.
The Analysis
Authors: Matthew Christopher A.
Published: July 2023

This chapter examines how Eratosthenes could have used a sundial to determine the angle of a shadow cast in Alexandria equivalent to 1/50 of the circumference of a circle (which is an integral part of his calculation of the circumference of the Earth). This was done by comparing the ratio of the distance between the base of the gnomon and the intersection of the noon and Summer Solstice lines on the face of the sundial for two instruments calibrated for two different locations (Alexandria and Syene). The concludes with a number of sections which individually examine the potential errors that are inherent in the assumed knowledge that Eratosthenes was working from, and other forms of error within the experiment, to determine their impact on the resultant calculations. This examination demonstrates that all of the potential sources of error had such a minimal impact of Eratosthenes’ result as to be negligible.
Selection, naturally and otherwise
Authors: Cutter Asher D.
Published: July 2023

Shows how evolution gets mediated by natural selection, artificial selection, and sexual selection. Considers timescales of evolution to demonstrate time as measured in generations rather than in years. Explores examples of adaptation from nature and from laboratory experiments that are informed by both molecular genetics and quantitative genetics, including cases of pigeons, coelacanth, race horses, finches, viruses, and moths. Discusses cryptic evolution that is nonetheless easy to prove by examining DNA in genomes. Explains how selection on sex and reproduction, not just survival, can lead to dramatic elaborations of traits. Explains the logic of fitness, heritability, and how humans can mold genetic variation to direct the course of evolutionary change.
Evolutionary accelerants and speed bumps
Authors: Cutter Asher D.
Published: July 2023

Explains the factors that help or hinder the speed of evolution. Documents the roles of genetic variation, genetic interactions, mutation, population size, and sex in speeding evolution along. Considers the evolutionary virtues of being small. Demystifies how genetic complications influence the pace of evolution, including the multiple pleiotropic effects that mutations can have and the tethering of effects of adjacent genes because of their linear arrangement in DNA. Explains the causes of correlated evolutionary changes to untargeted heritable characteristics, whether involving one gene or thousands of genes. Illustrates the merits of a selection index in artificial selection as a composite metric of all traits of interest. Examples feature tomatoes, Dalmatians, tardigrade water bears, and human height. Shows how new genetic novelty enters into a species, and how humans can influence the production of genetic novelty with genetic engineering.
Hijacking genetics
Authors: Cutter Asher D.
Published: July 2023

Explains how people can edit the DNA sequences of genomes using CRISPR-Cas9 genome editing and other biotechnologies. Describes how CRISPR-Cas9 itself evolved as a bacterial immune system and how its co-option by humans exploits cellular mechanisms of DNA repair. Explores how humans can intervene into evolution using genetic engineering techniques based on CRISPR-Cas9 genome editing or more basic methods of introducing mutations. Some genome editing is transgenic, adding DNA from another species, whereas some genome editing is cisgenic, using DNA sequences from other members of the same species. Examples highlight pigs and Caenorhabditis nematode roundworms. Shows how in vitro fertilization and cloning techniques intersect with the genetic manipulation with CRISPR-Cas9, and how people can apply them to mammals and birds alike.
Do-it-yourself speciation
Authors: Cutter Asher D.
Published: July 2023

Describes how human intervention through genetic engineering can recapitulate the origin of species. Considers the limits to depending on pre-existing genetic variation for creating new species barriers. Fruit flies illustrate how CRISPR-Cas9 genome editing can assist in engineering genetic incompatibilities as synthetic species boundaries. Illustrates how humans can create evolutionary novelty by directing evolution. Uses examples from industrial applications that direct evolution in synthetic vanilla production, synthetic biology construction of microbes that can make proteins with “unnatural” amino acids, and how people might go about giving hen teeth. Begins to outline some of the hazards and limitations of artificial selection and evolutionary engineering.
Evolving Deterrence Requirements
Authors: Baylis John , Eames Anthony
Published: July 2023

Détente and the development of superpower arms control generated a technological arms race that forced deterrence requirements to evolve. Franco-American nuclear cooperation concealed from the British and the independent dimensions of the UK Chevaline programme highlighted the continuing ‘mistrust within trust’ in the Anglo-American nuclear relationship. British investments in its own indigenous weapons system provided it with a technical choice, but the budget and political issues associated with going it alone made the US Trident weapons system a much more appealing option. Securing Trident required deft diplomacy, as the US was in the midst of a change in foreign policy philosophy due to the fallout over Vietnam and the demands of superpower arms control.
A methodology for designing a narrative generator based on problem-solving
Authors: Pérez Rafael Pérez y , Sharples Mike
Published: July 2023

This chapter introduces a four-step methodology for developing a narrative generator based on problem-solving: (1) Choose a main problem that a character must solve; this is known as the driving goal. (2) Develop the story’s outline where the driving goal is the core motivation. (3) Using the outline as a reference, build a goal-oriented plot graph (GOP-graph). (4) Employ the goal-oriented plot graph as a guideline to define the characteristics of the story-world and the attributes of the data structures. Our methodology starts with a very general idea, which is refined little by little, until we can specify the data structures to be used in the program. We introduce the concept of nested goals and explain the use of rules when defining goals.
Mexica
Authors: Pérez Rafael Pérez y , Sharples Mike
Published: July 2023

In this chapter we introduce the general characteristics of our proposal known as the engagement and reflection cognitive account of creative writing. During engagement the writer devotes full attention to creating a chain of associated ideas and turning them into text. During reflection the writer reviews the written material, invokes memories, transforms ideas, and identifies what new material to create. We explain how this proposal shapes the design of our computer model for narrative generation. Then we describe MEXICA, a realization of this model. The program produces outlines of short stories about the Mexicas, the former inhabitants of what today is México City. The program represents the emotional relations and the conflicts that are established between characters as the story develops. These representations are the key element to progress the plot. We provide a detailed example of how it works, and describe some of its main features, like its capacity to produce collaborative narratives and evaluate its own outputs.
Profiles of bacterial communities and environmental factors associated with proliferation of malaria vector mosquitoes within the Kenyan Coast
Authors: Mutinda Josphat , Mwamburi Samuel Mwakisha , Oduor Kennedy Omondi , Omolo Maurice O. , Ntabo Regina Mongina , Gathiru James Muhunyu , Mwangangi Joseph , Nonoh James O.M
Published: July 2023

Abstract

Background
Since Anopheles mosquitoes which transmit and maintain the malaria parasite breed in the outdoor environment, there is an urgent need to manage these mosquito breeding sites. In order to elaborate more on the ecological landscape of mosquito breeding sites, the bacterial community structure and their interactions with physicochemical factors in mosquito larval habitats was characterised in Kwale County (Kenya), where malaria is endemic.
Materials and methods
The physical characteristics and water physicochemical parameters of the habitats were determined and recorded. Water samples were also collected from the identified sites for total metagenomic DNA extraction in order to characterise the bacterial communities within the breeding sites.
Results and Discussion
Sites where mosquito larvae were found were described as positive and those without mosquito larvae as negative. Electrical conductivity, total dissolved solids, salinity and ammonia were lower in the rainy season than in the dry season, which also coincided with a high proportion of positive sites.  Pseudomonadota was the most common phyla recovered in all samples followed by Bacteroidota and then Actinomycetota. The presence or absence of mosquito larvae in a potential proliferation site was not related to the bacterial community structure in the sampled sites, but was positively correlated with bacterial richness and evenness.
Conclusion
Generally, the presence of Anopheles mosquito larvae was found to be positively correlated with rainy season, bacterial richness and evenness, and negatively correlated with electrical conductivity, total dissolved solids, salinity and ammonia. The findings of this study have implications for predicting the potential of environmental water samples to become mosquito proliferation sites.
Probing thein-situvolumes of Arabidopsis leaf plastids using 3D confocal and scanning electron microscopy
Authors: Knoblauch Jan , Waadt Rainer , Cousins Asaph B. , Kunz Hans-Henning
Published: July 2023

Leaf plastids harbor a plethora of biochemical reactions including photosynthesis, one of the most important metabolic pathways on earth. Scientists are eager to unveil the physiological processes within the organelle but also their interconnection with the rest of the plant cell. An increasingly important feature of this venture is to use experimental data in the design of metabolic models. A remaining obstacle has been the limited in situ volume information of plastids and other cell organelles. To fill this gap for chloroplasts, we established three microscopy protocols deliveringin situvolumes based on: 1) chlorophyll fluorescence emerging from the thylakoid membrane, 2) a CFP marker embedded in the envelope, and 3) calculations from serial block-face scanning electron microscopy (SBFSEM). The obtained data were corroborated by comparing wild-type data with two mutant lines affected in the plastid division machinery known to produce small and large mesophyll chloroplasts, respectively. Furthermore, we also determined the volume of the much smaller guard cell plastids. Interestingly, their volume is not governed by the same components of the division machinery which defines mesophyll plastid size. Based on our three approaches the average volume of a mature Col-0 wild-type mesophyll chloroplasts is 93 µm3. Wild-type guard cell plastids are approximately 18 µm3. Lastly, our comparative analysis shows that the chlorophyll fluorescence analysis can accurately determine chloroplast volumes, providing an important tool to research groups without access to transgenic marker lines expressing genetically encoded fluorescence proteins or costly SBFSEM equipment.

Significance statement -sentence summary

This work describes and compares three different strategies to obtain accurate volumes of leaf plastids from Arabidopsis, the most widely used model plant. We hope our contribution will support quantitative metabolic flux modeling and spark other projects aimed at a more metric-driven plant cell biology.
Identification and Description of Emotions by Current Large Language Models
Authors: Patel Suketu C. , Fan Jin
Published: July 2023

The assertion that artificial intelligence (AI) cannot grasp the complexities of human emotions has been a long-standing debate. However, recent advancements in large language models (LLMs) challenge this notion by demonstrating an increased capacity for understanding and generating human-like text. In this study, we evaluated the empathy levels and the identification and description of emotions by three current language models: Bard, GPT 3.5, and GPT 4. We used the Toronto Alexithymia Scale (TAS-20) and the 60-question Empathy Quotient (EQ-60) questions to prompt these models and score the responses. The models’ performance was contrasted with human benchmarks of neurotypical controls and clinical populations. We found that the less sophisticated models (Bard and GPT 3.5) performed inferiorly on TAS-20, aligning close to alexithymia, a condition with significant difficulties in recognizing, expressing, and describing one’s or others’ experienced emotions. However, GPT 4 achieved performance close to the human level. These results demonstrated that LLMs are comparable in their ability to identify and describe emotions and may be able to surpass humans in their capacity for emotional intelligence. Our novel insights provide alignment research benchmarks and a methodology for aligning AI with human values, leading toward an empathetic AI that mitigates risk.
The Genomic Legacy of Aurochs hybridization in ancient and modern Iberian Cattle
Authors: Günther Torsten , Chisausky Jacob , Galindo-Pellicena M. Ángeles , Iriarte Eneko , Gardyn Oscar Cortes , Eusebi Paulina G. , García-González Rebeca , Urena Irene , Moreno Marta , Alday Alfonso , Rojo Manuel , Pérez Amalia , Rodríguez Cristina Tejedor , de Lagrán Iñigo García Martínez , Arsuaga Juan Luis , Carretero José-Miguel , Götherström Anders , Smith Colin , Valdiosera Cristina
Published: July 2023

Cattle have been a valuable economic resource and cultural icon since prehistory. From the initial expansion of domestic cattle into Europe during the Neolithic period, taurine cattle (Bos taurus) and their wild ancestor, the aurochs (B. primigenius), had overlapping ranges, leading to ample opportunities for mating (whether intended by farmers or not). We performed a bioarchaeological analysis of 24 Bos remains from Iberia dating from the Mesolithic to the Roman period. The archaeogenomic dataset allows us to investigate the extent of domestic-wild hybridization over time, providing insight into the species’ behavior and human hunting and management practices by aligning changes with cultural and genomic transitions in the archaeological record. Our results show frequent hybridization during the Neolithic and Chalcolithic, likely reflecting a mix of hunting and herding or relatively unmanaged herds, with mostly male aurochs and female domestic cattle involved in hybridization. This is supported by isotopic evidence consistent with ecological niche sharing, with only a few domestic cattle possibly being managed. The proportion of aurochs ancestry remains relatively constant from about 4000 years ago, probably due to herd management and selection against first generation hybrids, coinciding with other cultural transitions. The constant level of wild ancestry (∽20%) continues into modern western European breeds including the Spanish Lidia breed which is bred for its aggressiveness and fighting ability, but does not display elevated levels of aurochs ancestry. This study takes a genomic glance at the impact of human actions and wild introgression in the establishment of cattle as one of the most important domestic species today.
Human Cytomegalovirus in breast milk is associated with milk composition, the infant gut microbiome, and infant growth
Authors: Johnson Kelsey E. , Heisel Timothy , Fields David A. , Isganaitis Elvira , Jacobs Katherine M. , Knights Dan , Lock Eric F. , Rudolph Michael C. , Gale Cheryl A. , Schleiss Mark R. , Albert Frank W. , Demerath Ellen W. , Blekhman Ran
Published: July 2023

Human cytomegalovirus (CMV) is a highly prevalent herpesvirus that is often transmitted to the neonate via breast milk. Postnatal CMV transmission can have negative health consequences for preterm and immunocompromised infants, but any effects on healthy term infants are thought to be benign. Furthermore, the impact of CMV on the composition of the hundreds of bioactive factors in human milk has not been tested. Here, we utilize a cohort of exclusively breastfeeding full term mother-infant pairs to test for differences in the milk transcriptome and metabolome associated with CMV, and the impact of CMV in breast milk on the infant gut microbiome and infant growth. We find upregulation of the indoleamine 2,3-dioxygenase (IDO) tryptophan-to-kynurenine metabolic pathway in CMV+ milk samples, and that CMV+ milk is associated with decreasedBifidobacteriumin the infant gut. Our data indicate a complex relationship between milk CMV, milk kynurenine, and infant growth; with kynurenine positively correlated, and CMV viral load negatively correlated, with infant weight-for-length at 1 month of age. These results suggest CMV transmission, CMV-related changes in milk composition, or both may be modulators of full term infant development.
Identification of the active mechanism of aminoglycoside entry inV. choleraethrough characterization of sRNActrR,regulating carbohydrate utilization and transport
Authors: Pierlé Sebastian A. , Lang Manon , López-Igual Rocío , Krin Evelyne , Fourmy Dominique , Kennedy Sean P. , Val Marie-Eve , Baharoglu Zeynep , Mazel Didier
Published: July 2023

The possible active entry of aminoglycosides in bacterial cells has been debated since the development of this antibiotic family. Here we report the identification of their active transport mechanism inVibriospecies. We combined genome-wide transcriptional analysis and fitness screens to identify alterations driven by treatment ofV. choleraewith sub-minimum inhibitory concentrations (sub-MIC) of the aminoglycoside tobramycin. RNA-seq data showed downregulation of the small non-coding RNAncRNA586during such treatment, while Tn-seq revealed that inactivation of this sRNA was associated with improved fitness in the presence of tobramycin. This sRNA is located near sugar transport genes and previous work on a homologous region inVibrio tasmaniensissuggested that this sRNA stabilizes gene transcripts for carbohydrate transport and utilization, as well as phage receptors. The role forncRNA586, hereafter namedctrR, in the transport of both carbohydrates and aminoglycosides, was further investigated. Flow cytometry on cells treated with a fluorescent aminoglycoside confirmed the role ofctrRand of carbohydrate transporters in differential aminoglycoside entry. Despite sequence diversity,ctrRshowed functional conservation across the Vibrionales. This system in directly modulated by carbon sources, suggesting regulation by carbon catabolite repression, a widely conserved mechanism in Gram-negative bacteria, priming future research on aminoglycoside uptake by sugar transporters in other bacterial species.
Exploring the molecular makeup of support cells in insect camera eyes
Authors: Rathore Shubham , Stahl Aaron , Benoit Joshua B. , Buschbeck Elke K.
Published: July 2023

Animals generally have either compound eyes, which have evolved repeatedly in different invertebrates, or camera eyes, which have evolved many times across the animal kingdom. Both eye types include two important kinds of cells: photoreceptor cells, which can be excited by light, and non-neuronal support cells (SupCs), which provide essential support to photoreceptors. Despite many examples of convergence in eye evolution, similarities in the gross developmental plan and molecular signatures have been discovered, even between phylogenetically distant and functionally different eye types. For this reason, a shared evolutionary origin has been considered for photoreceptors. In contrast, only a handful of studies, primarily on the compound eyes ofDrosophila melanogaster, have demonstrated molecular similarities in SupCs.D. melanogasterSupCs (Semper cells and primary pigment cells) are specialized eye glia that share several molecular similarities with certain vertebrate eye glia, including Müller glia. This led us to speculate whether there are conserved molecular signatures of SupCs, even in functionally different eyes such as the image-forming larval camera eyes of the sunburst diving beetleThermonectus marmoratus. To investigate this possibility, we used an in-depth comparative whole-tissue transcriptomics approach. Specifically, we dissected the larval principal camera eyes into SupC- and retina-containing regions and generated the respective transcriptomes. Our analysis revealed several conserved features of SupCs including enrichment of genes that are important for glial function (e.g. gap junction proteins such as innexin 3), glycogen production (glycogenin), and energy metabolism (glutamine synthetase 1 and 2). To evaluate the extent of conservation, we compared our transcriptomes with those of fly (Semper cells) and vertebrate (Müller glia) eye glia as well as respective retinas.T. marmoratusSupCs were found to have distinct genetic overlap with both fly and vertebrate eye glia. These results provide molecular evidence for the deep conservation of SupCs in addition to photoreceptor cells, raising essential questions about the evolutionary origin of eye-specific glia in animals.
Analysis ofDrosophilaand mouse mutants reveals that Peroxidasin is required for tissue mechanics and full viability
Authors: Peebles K. Elkie , LaFever Kimberly S. , Page-McCaw Patrick S. , Colon Selene , Wang Dan , Stricker Aubrie M. , Ferrell Nicholas , Bhave Gautam , Page-McCaw Andrea
Published: July 2023

Basement membranes are thin strong sheets of extracellular matrix. They provide mechanical and biochemical support to epithelia, muscles, nerves, and blood vessels, among other tissues. The mechanical properties of basement membranes are conferred in part by Collagen IV (Col4), an abundant protein of basement membrane that forms an extensive two-dimensional network through head-to-head and tail-to-tail interactions. After the Col4 network is assembled into a basement membrane, it is crosslinked by the matrix-resident enzyme Peroxidasin to form a large covalent polymer. Peroxidasin and Col4 crosslinking are highly conserved, indicating they are essential, but homozygous mutant mice have mild phenotypes. To explore the role of Peroxidasin, we analyzed mutants in Drosophila, including a newly generated catalytic null, and found that homozygotes were mostly lethal with 13% viable escapers. A Mendelian analysis of mouse mutants shows a similar pattern, with homozygotes displaying ∼50% lethality and ∼50% escapers. Despite the strong mutations, the homozygous escapers had low but detectable levels of Col4 crosslinking, indicating that inefficient alternative mechanisms exist and that are probably responsible for the viable escapers. Further, fly mutants have phenotypes consistent with a decrease in stiffness. Interestingly, we found that even after adult basement membranes are assembled and crosslinked, Peroxidasin is still required to maintain stiffness. These results suggest that Peroxidasin crosslinking may be more important than previously appreciated.
Chainsaw: protein domain segmentation with fully convolutional neural networks
Authors: Wells Jude , Hawkins-Hooker Alex , Bordin Nicola , Sillitoe Ian , Paige Brooks , Orengo Christine
Published: July 2023

0.1

Motivation

Protein domains are fundamental units of protein structure and play a pivotal role in understanding folding, function, evolution, and design. The advent of accurate structure prediction techniques has resulted in an influx of new structural data, making the partitioning of these structures into domains essential for inferring evolutionary relationships and functional classification.

0.2

Results

This manuscript presents Chainsaw, a supervised learning approach to domain parsing that achieves accuracy that surpasses current state-of-the-art methods. Chainsaw uses a fully convolutional neural network which is trained to predict the probability that each pair of residues is in the same domain. Domain predictions are then derived from these pairwise predictions using an algorithm that searches for the most likely assignment of residues to domains given the set of pairwise co-membership probabilities. Chainsaw matches CATH domain annotations in 78% of protein domains versus 72% for the next closest method. When predicting on AlphaFold models expert human evaluators were twice as likely to prefer Chainsaw’s predictions versus the next best method.

0.3

Availability and Implementation

Code implementation of Chainsaw is available atgithub.com/JudeWells/chainsaw.
Intraoperative lung ultrasound improves subcentimetric pulmonary nodule localization during VATS: Results of a retrospective analysis
Authors: Gambardella Claudio , Messina Gaetana , Pica Davide Gerardo , Bove Mary , Capasso Francesca , Mirra Rosa , Natale Giovanni , D'Alba Francesco Panini , Caputo Alessia , Leonardi Beatrice , Puca Maria Antonietta , Giorgiano Noemi Maria , Pirozzi Mario , Farese Stefano , Zotta Alessia , Miele Francesco , Vicidomini Giovanni , Docimo Ludovico , Fiorelli Alfonso , Ciardiello Fortunato , Fasano Morena
Published: July 2023

Background

Video‐assisted thoracoscopic surgery (VATS) resection of deep‐seated lung nodules smaller than 1 cm is extremely challenging. Several methods have been proposed to overcome this limitation but with not neglectable complications. Intraoperative lung ultrasound (ILU) is the latest minimally invasive proposed technique. The aim of the current study was to analyze the accuracy and efficacy of ILU associated with VATS to visualize solitary and deep‐seated pulmonary nodules smaller than 1 cm.

Methods

Patients with subcentimetric solitary and deep‐seated pulmonary nodules were included in this retrospective study from November 2020 to December 2022. Patients who received VATS aided with ILU were considered as group A and patients who received conventional VATS as group B (control group). The rate of nodule identification and the time for localization with VATS alone and with VATS aided with ILU in each group were analyzed.

Results

A total of 43 patients received VATS aided with ILU (group A) and 31 patients received conventional VATS (group B). Mean operative time was lower in group A (p < 0.05). In group A all the nodules were correctly identified, while in group B in one case the localization failed. The time to identify the lesion was lower in group A (7.1 ± 2.2 vs. 13.8 ± 4.6; p < 0.05). During hospitalization three patients (6.5%; p < 0.05) in group B presented air leaks that were conservatively managed.

Conclusion

Intracavitary VATS‐US is a reliable, feasible, real‐time and effective method of localization of parenchymal lung nodules during selected wedge resection procedures.
Mind and skin: Exploring the links between inflammation, sleep disturbance and neurocognitive function in patients with atopic dermatitis
Authors: Cameron Shona , Donnelly Ali , Broderick Conor , Arichi Tomoki , Bartsch Ullrich , Dazzan Paola , Elberling Jesper , Godfrey Emma , Gringras Paul , Heathcote Lauren C. , Joseph Desaline , Wood Tobias C. , Pariante Carmine , Rubia Katya , Flohr Carsten
Published: July 2023

Atopic dermatitis (AD) is a chronic, pruritic and inflammatory, dry skin condition with many known comorbidities. These include airway disease, food allergies, atopic eye disease and autoimmune conditions. Furthermore, there is often significant sleep disturbance as well as increased psychological distress and mental health problems. Severe AD therefore often has a significant impact on the quality of life of both patients and their families. In this review we discuss recent findings on the putative links between AD, its association with itch, sleep disturbance and neuropsychiatric morbidity, including the role of inflammation in these conditions. Itch was thought to predominantly drive sleep disruption in AD. We now understand changes in sleep influence immune cell distribution and the associated inflammatory cytokines, which suggests a bidirectional relationship between AD and sleep. We also increasingly recognize inflammation as a key driver in psychological symptoms and disorders. The link between cutaneous, systemic and possible brain inflammation could at least in part be driven by the sleep deprivation and itch‐driven neuronal proliferation seen in AD.
MPP2 interacts with SK2 to rescue the excitability of glutamatergic neurons in the BLA and facilitate the extinction of conditioned fear in mice
Authors: Peng Xiaohan , Chen Panpan , Zhang Yang , Wu Ke , Ji Ningning , Gao Jinghua , Wang Hui , Zhang Yong‐mei , Xu Tie , Hua Rong
Published: July 2023

Aims

The basolateral amygdala (BLA) plays an integral role in anxiety disorders (such as post traumatic stress disorder) stem from dysregulated fear memory. The excitability of glutamatergic neurons in the BLA correlates with fear memory, and the afterhyperpolarization current (IAHP) mediated by small‐conductance calcium‐activated potassium channel subtype 2 (SK2) dominates the excitability of glutamatergicneurons. This study aimed to explore the effect of MPP2 interacts with SK2 in the excitability of glutamatergic neurons in the BLA and the extinction of conditioned fear in mice.

Methods

Fear memory was analyzed via freezing percentage. Western blotting and fluorescence quantitative PCR were used to determine the expression of protein and mRNA respectively. Electrophysiology was employed to measure the excitability of glutamatergic neurons and IAHP.

Results

Fear conditioning decreased the levels of synaptic SK2 channels in the BLA, which were restored following fear extinction. Notably, reduced expression of synaptic SK2 channels in the BLA during fear conditioning was caused by the increased activity of protein kinase A (PKA), while increased levels of synaptic SK2 channels in the BLA during fear extinction were mediated by interactions with membrane‐palmitoylated protein 2 (MPP2).

Conclusions

Our results revealed that MPP2 interacts with the SK2 channels and rescues the excitability of glutamatergic neurons by increasing the expression of synaptic SK2 channels in the BLA to promote the normalization of anxiety disorders and provide a new direction for the treatment.