bluuebunny/crossref_metadata_2025_split huggingface dataset:
Units
Authors: James Patrick 
Published: December 2022

Abstract
Units are conveyed in detail in Chapter 5. Two units are included. The first concerns rationality. Actors within the metatheory are assumed to follow self-interest, that is, instrumental rationality. This contrasts to normative rationality, which would assess behavior on the basis of a moral standard. The second type of unit is the system of explanation, which refers to encompassing entities such as paradigms or research programs that provide an organizing principle for a given discipline. After a review of existing options regarding systems of explanation, a synthesis is developed: the research enterprise. The concept of a research enterprise brings together the best aspects of (i) inductive and sociological and (ii) deductive and rationalist predecessors among systems of explanation. Creation of the research enterprise as an amalgam of positive features from systems of explanation that have found significant application in IR reflects a commitment to analytic eclecticism.
Methods
Authors: James Patrick 
Published: December 2022

Abstract
Chapter 6 presents the two methods—identification of axioms for a research enterprise and systemism—entailed within the metatheory. The first focuses on how assumptions are designated to create the foundation for a given research enterprise within IR. Axioms are selected through a process that includes deductive and inductive reasoning. In this way, rigorous standards for designating assumptions are combined with a realistic description of how members of a research community see themselves. The other method, systemism, is a visual technique for conveying theories in a way that facilitates comparison and criticism. Systemism emphasizes completeness and logical consistency regarding cause and effect within and across levels of analysis, along with recognition of how a system and its environment are linked to each other. The chapter also introduces Systemist International Relations (SIR), which includes a method for graphic portrayal of expositions on an individual basis and in combination with each other.
Predation
Authors: James Patrick 
Published: December 2022

Abstract
Chapter 18 introduces predation theory, the most recent among realist expositions on the causes of war. This theory puts forward an explanation for war that focuses on the dynamics of relative capability between and among the great powers. Predation theory assumes, with justification, that leaders rarely possess fully accurate information about the distribution of power. Policies among rising states therefore will vary by context; there is no deterministic pathway to either peace or war under conditions of strategically significant change in relative capabilities. Predation theory seeks to “understand and account for a rising state’s predatory or supportive policies toward its declining peers.” The focus is on the politics associated with power shifts. Predation theory seeks to explain the degree of conflict observed during times of significant change in relative capabilities. War becomes more likely under such circumstances.
Realism and Progress in International Relations
Authors: James Patrick 
Published: December 2022

Abstract
Chapter 20 reflects on the project as a whole and gets underway with a review of specific accomplishments from Parts I–IV and Chapter 19. This final chapter assesses realism in an overall sense in light of an extensive graphic review of its theories in the context of the causes of war. Is realism a scientifically viable research enterprise? This question is answered affirmatively, but tentatively. Potential exists but remains unrealized for realism, which must meet rather than eschew scientific standards in order to move forward. Accomplishment of that goal through adoption of a systemist graphic approach to communication, in turn, would facilitate comparison to any other research enterprise that subsequently is identified in the same way as for realism within this volume. The chapter also offers several ideas about future research, and its final thoughts are on the prospects of realism as a scientific research enterprise.
Dark Secrets of the Crystal Maiden
Authors: Pauketat Timothy R. 
Published: December 2022

Abstract
The transition from to the warmer and drier conditions of the medieval period in the Yucatan Peninsula of southern Mexico saw the end of the Classic Maya civilization. That earlier civilization was based around the exclusive rights of elites to intercede with cosmic forces on behalf of ordinary Maya farmers. Classic jungle cities such as Tikal, with its tall white pyramids, were grand theaters for royalty to commune with the gods, especially Chahk, the lord of water and rain. But the aristocratic ways were undermined by medieval climate change, and new religious and political movements fomented, pulling people and their beliefs away from the cities of Classic-period rulers and toward the caves, natural pools, and springs where ordinary people traveled to worship inside the dark interiors of circular shrines. Marine shells and human sacrifices left in such places bespeak the intimate relationships between people and the forces of climate change.
Across the Chichimec Sea
Authors: Pauketat Timothy R. 
Published: December 2022

Abstract
The religious movements of Mesoamerican inspiration extended well up into the Great Plains of North America, where a young man named Black Elk in the late 1800s would continue the worship of gods he knew as Thunderers. The Sun Dance and sweat lodge ceremonialism there were rooted in medieval-era Mesoamerica. The Mesoamerican practices, in turn, emerged from an even earlier worship of storms, clouds, and volcanoes coeval with the great imperial city of Teotihuacan. These places included Cuicuilco, all but its tallest circular pyramids buried in lava 1600 or more years ago. And they included Los Guachimontónes, circular pyramids that were the bases for early pole-flying ceremonies.
The Other Corn Road
Authors: Pauketat Timothy R. 
Published: December 2022

Abstract
Circular platforms of earth connect the Caddo peoples of Texas, Oklahoma, Arkansas, and Louisiana with the Huastecs of northeastern Mesoamerica in the 900s. They shared with Chaco and the soon-to-appear city of Cahokia a fascination with lunar calendrics, alignment, the ceremonial use of hallucinogenic drugs, and the elaborate decoration of certain pottery vessels. All are evident at Formative Caddo sites such as Crenshaw and the George C. Davis site. With Mesoamerica, the Caddo people also shared the practice of human sacrifice. Some early Caddo people probably migrated to Cahokia and may have been conduits for the introduction of such practices, along with the all-important Mesoamerican and Southwestern maize plant, into eastern North America.
The Quinean Legacy
Authors: Stalnaker Robert 
Published: December 2022

Abstract
This chapter provides an interpretation of W. V. Quine’s methodology and metaphysical theory, in order to provide a background for the neo-Quinean theory of propositions that will be developed later in the book. It emphasizes Quine’s naturalism (his rejection of a transcendent a priori perspective from which to do philosophy) and his way of characterizing the project of regimentation (the construction of a formal language for representing one’s philosophical and scientific commitment). It discusses Quine’s distinctions between ontology and meta-ontology, and between the commitments of logic and the substantive commitments of a specific regimented theory. In the discussion of Quine’s views about logic, it considers the logical status of identity theory and of set theory, and the role of singular terms.
Possible Worlds and Possible Individuals
Authors: Stalnaker Robert 
Published: December 2022

Abstract
While this book endorses an ontological commitment to propositions, properties, and relations, it rejects a commitment to the existence of merely possible worlds or merely possible individuals. The aim of this chapter is to reconcile the rejection of these ontological commitments with a model theory for modal logic that seems to require them. It is argued that a model structure of a Kripke model that is intended to represent some aspect of reality should be regarded as a representational device that may contain artifacts that do not correspond to anything in the reality being modeled. The role of the artifacts is to represent a relational structure that is realized in the domains of entities being modeled. The modeling strategy is a generalized supervaluation strategy that uses refinements of models to facilitate the compositional semantics for domains with relational structure that is not grounded intrinsic properties.
Forests
Authors: Seligson Kenneth E. 
Published: December 2022

Abstract
This chapter focuses on Classic Maya forest-management practices. The forest was more than a living pantry for the Classic Maya—it was also a living hardware store, pharmacy, and recreation center, all rolled into one. The modern forest compositions of the Maya lowlands have been heavily shaped by generations of knowledgeable agroforesters who promoted the growth of the most useful plants for food, lumber, fuel, medicine, and many other purposes. Researchers use paleoenvironmental analyses including pollen, charcoal, and erosion analyses, as well as ethnohistoric and ethnographic analogies to understand how ancient Maya communities exploited and conserved their resources. Classic Period communities developed forest-management practices that included shaping and tending the young forests that sprung up from fallowed fields as well as conserving valuable sapodilla and other trees in old growth forests. Despite careful maintenance, fallow periods likely grew increasingly truncated toward the end of the Classic Period to allow communities to sustain continuous population growth. The socio-ecological symbiosis established among city, forest, and field over the course of the Early and Middle Classic Periods gave way to an increasing proportion of land being used for agriculture. The difficulty of maintaining the forest-conservation strategies that had worked so well for centuries was compounded in the eighth and ninth centuries by climatic and socio-political crises. Paleoenvironmental data indicate that many communities addressed the challenges of that turbulent era by adapting their forest exploitation practices to focus on different fuel sources and regenerating certain species.
Stone
Authors: Seligson Kenneth E. 
Published: December 2022

Abstract
This chapter explores how the production of burnt lime and salt by Classic Maya communities intersected with forest-resource-management strategies. Stone-processing techniques and trajectories varied greatly across the Classic lowlands. Communities with larger civic-ceremonial complexes and populations like Tikal and Caracol required much more lime and salt on an annual basis than smaller polities like Copan or Aguateca. Frequencies of masonry architecture construction likewise varied between communities and subregions. There were likely pronounced differences in production and procurement of lime between urban and rural contexts. Although some sites were able to manage their natural resources better than others, it is clear that communities throughout the lowlands adapted new lime-production practices over the course of the Classic Period to meet the challenges of changing environmental, socio-political, and climatic conditions. Like lime production, the bulk of the salt production (at least in the southern lowlands) would have required significant amounts of wood fuel. Producers in the interior and along the coasts developed methods to maximize their fuel efficiency and exhibited a capacity to adapt their fuel use when circumstances required it. Increasingly detailed investigations of Pre-Colonial lime and salt production are contributing to a more nuanced understanding of Classic Maya communities as proactive and successful natural resource managers.
Legal Philosophy and the Nature of Law
Authors: Dickson Julie 
Published: December 2022

Abstract
This chapter considers some important contemporary challenges to legal philosophy about the nature of law. The challenges in question respectively allege that legal philosophy about the nature of law is: theoretically imperialist; guilty of guild exclusivity; impossible; too abstract/neglectful of law’s social character; committed to addressing static, staple questions. The chapter engages with each of these challenges in turn, in order to attain a clearer understanding of each challenge and better to appreciate which of them can be dealt with largely within the confines of this chapter, and which of them demand a fuller response which will emerge from the book as a whole. In engaging with these challenges, the chapter also further fleshes out and renders plausible an appropriately metaphysically modest and domain-apt understanding of what it is for law to have a nature that one important part of legal philosophy seeks to explain.
The Questions of Legal Philosophy
Authors: Dickson Julie 
Published: December 2022

Abstract
The focus of this chapter lies not with the answers legal philosophers offer to questions concerning law’s nature, but with the diversity of and developments in the questions they ask, and the leeway they have in selecting which questions to address and how to address them. The chapter argues that there is room for significant, and welcome, ‘question pluralism’ within legal philosophy about the nature of law, and that we should embrace the fact that the many and varied questions legal philosophers address are shaped by and responsive to the time and context in which they arise. The chapter discusses two roles for choice in theory construction in legal philosophy: subject-matter selectivity and distribution of emphasis selectivity. By the chapter’s close, the discussion establishes that legal philosophy about the nature of law is not an enterprise that addresses problematically static, staple questions. Rather, it is a dynamic enterprise involving changing, developing, and diversifying questions the answers to which can reveal distinctive truths about the many facets of law’s nature.
Defining Identity
Authors: Razzack Azra , Siddiqui M. Atyab 
Published: December 2022

Abstract
Chapter IV Defining Identity essentially defines the identity of the school. The school life is projected through a discussion of what the school has to offer its students, the community it serves, school life, and campus stories. There is a discussion on the school’s logo and motto—‘Find a Way or Make One’, Etimadiah, the school magazine, and so on. ‘The school in verse’ section presents some of the poems and verses written about the school by its students and teachers which have appeared in the school magazines over the years as well as the school Tarana composed by Gulzar Dehalvi. It also tells us about the community the school serves, and life at school. The identity of the institution is what makes it special.
The Girls Arrive
Authors: Razzack Azra , Siddiqui M. Atyab 
Published: December 2022

Abstract
Chapter VIII, The Girls Arrive, tells the story of converting the Anglo Arabic from an only boys school to being a co-educational institution. The controversy generated and the challenges presented are highlighted in an absorbing account. What admission to the school meant for the girls themselves is also captured here. History has witnessed that change is born in conflict. Even for a reformatory step like opening the school to the girl child, the administrators had to struggle. Surprisingly, the teachers who are supposed to be advocates of change opposed the admission of girls in the institution. The principal too had to be taken to task for this opposition. The local politicians went up in arms, and it required an order from the law court to firmly establish it as a co-educational institution. The girls justified their admission by securing flying colours in the Board examination. A new chapter had been introduced in the history of the institution.
Protocol for Biospecimen Collection and Analysis Within the BACPAC Research Program
Authors: Fields Aaron J , Dudli Stefan , Schrepf Andrew , Kim Angie , Pham Bernice , Gallego Estefania , Mendoza Sandra , Meropol Sharon B , Darwin Jessa , Sowa Gwendolyn , Vo Nam V 
Published: December 2022

Abstract
The Biospecimen Collection and Processing Working Group of the National Institutes of Health (NIH) HEAL Initiative BACPAC Research Program was charged with identifying molecular biomarkers of interest to chronic low back pain (cLBP). Having identified biomarkers of interest, the Working Group worked with the New York University Grossman School of Medicine, Center for Biospecimen Research and Development—funded by the Early Phase Pain Investigation Clinical Network Data Coordinating Center—to harmonize consortium-wide and site-specific efforts for biospecimen collection and analysis. Biospecimen collected are saliva, blood (whole, plasma, serum), urine, stool, and spine tissue (paraspinal muscle, ligamentum flavum, vertebral bone, facet cartilage, disc endplate, annulus fibrosus, or nucleus pulposus). The omics data acquisition and analyses derived from the biospecimen include genomics and epigenetics from DNA, proteomics from protein, transcriptomics from RNA, and microbiomics from 16S rRNA. These analyses contribute to the overarching goal of BACPAC to phenotype cLBP and will guide future efforts for precision medicine treatment.
Milk antibody response after 3rd dose of COVID-19 mRNA vaccine and SARS-CoV-2 breakthrough infection and implications for infant protection
Authors: Golan Yarden , Ilala Mikias , Gay Caryl , Hunagund Soumya , Lin Christine Y. , Cassidy Arianna G. , Jigmeddagva Unurzul , Li Lin , Ozarslan Nida , Asiodu Ifeyinwa V. , Ahituv Nadav , Flaherman Valerie J. , Gaw Stephanie L. , Prahl Mary 
Published: December 2022

AbstractAnti-SARS-CoV-2 antibodies have been found in human-milk after COVID-19 infection and vaccination. However, little is known about their persistence in milk after booster vaccination and breakthrough infection. In this study, human-milk, saliva and blood samples were collected from 33 lactating individuals before and after mRNA-based vaccination and COVID-19 breakthrough infections. Antibody levels were measured using ELISA and symptoms were assessed using questionnaires. Evaluation of maternal and infant symptomatology revealed that infected mothers reported more symptoms than vaccinated mothers. We found that after vaccination, human-milk anti-SARS-CoV-2 antibodies persisted for up to 8 months. In addition, distinct patterns of human milk IgA and IgG production we observed after breakthrough infection compared to 3-dose vaccination series alone, indicating a differential central and mucosal immune profiles in hybrid compared with vaccine-induced immunity. To investigate passively-derived milk antibody protection in infants, we examined the persistence of these antibodies in infant saliva after breastfeeding. We found that IgA was more abundant in infant saliva compared to IgG and persist in infant saliva longer after feeding. Our results delineate the differences in milk antibody response to vaccination as compared to breakthrough infection and emphasize the importance of improving the secretion of IgA antibodies to human milk after vaccination to improve the protection of breastfeeding infants.
Effective methods for bulk RNA-Seq deconvolution using scnRNA-Seq transcriptomes
Authors: Cobos Francisco Avila , Najaf Panah Mohammad Javad , Epps Jessica , Long Xiaochen , Man Tsz-Kwong , Chiu Hua-Sheng , Chomsky Elad , Kiner Evgeny , Krueger Michael J , Bernardo Diego di , Voloch Luis , Molenaar Jan , van Hooff Sander R. , Westermann Frank , Jansky Selina , Redell Michele L. , Mestdagh Pieter , Sumazin Pavel 
Published: December 2022

ABSTRACTRNA profiling technologies at single-cell resolutions, including single-cell and single-nuclei RNA sequencing (scRNA-Seq and snRNA-Seq, scnRNA-Seq for short), can help characterize the composition of tissues and reveal cells that influence key functions in both healthy and disease tissues. However, the use of these technologies is operationally challenging because of high costs and stringent sample-collection requirements. Computational deconvolution methods that infer the composition of bulk-profiled samples using scnRNA-Seq-characterized cell types can broaden scnRNA-Seq applications, but their effectiveness remains controversial. We produced the first systematic evaluation of deconvolution methods on datasets with either known or scnRNA-Seq-estimated compositions. Our analyses revealed biases that are common to scnRNA-Seq 10X Genomics assays and illustrated the importance of accurate and properly controlled data preprocessing and method selection and optimization. Moreover, our results suggested that concurrent RNA-Seq and scnRNA-Seq profiles can help improve the accuracy of both scnRNA-Seq preprocessing and the deconvolution methods that employ them. Indeed, our proposed method, Single-cell RNA Quantity Informed Deconvolution (SQUID), combined RNA-Seq transformation and dampened weighted least-squares deconvolution approaches to consistently outperform other methods in predicting the composition of cell mixtures and tissue samples. Furthermore, our analysis suggested that only SQUID could identify outcomes-predictive cancer cell subclones in pediatric acute myeloid leukemia and neuroblastoma datasets, suggesting that deconvolution accuracy improvements are vital to enabling its applications in the life sciences.
Machine Learning Reveals Genetic Modifiers of the Immune Microenvironment of Cancer
Authors: Riley-Gillis Bridget , Tsaih Shirng-Wern , King Emily , Wollenhaupt Sabrina , Reeb Jonas , Peck Amy R. , Wackman Kelsey , Lemke Angela , Rui Hallgeir , Dezso Zoltan , Flister Michael J. 
Published: December 2022

ABSTRACTHeritability in the immune tumor microenvironment (iTME) has been widely observed, yet remains largely uncharacterized and systematic approaches to discover germline genetic modifiers of the iTME still being established. Here, we developed the first machine learning approach to map iTME modifiers within loci from genome-wide association studies (GWAS) for breast cancer (BrCa) incidence and outcome. A random forest model was trained on a positive set of immune-oncology (I-O) targets using BrCa and immune phenotypes from genetic perturbation studies, comparative genomics, Mendelian genetics, and colocalization with autoimmunity and inflammatory disease risk loci. Compared with random negative sets, an I-O target probability score was assigned to the 1,362 candidate genes in linkage disequilibrium with 155 BrCa GWAS loci. Pathway analysis of the most probable I-O targets revealed significant enrichment in drivers of BrCa and immune biology, including theLSP1locus associated with BrCa incidence and outcome. Quantitative cell type-specific immunofluorescent imaging of 1,109 BrCa patient biopsies revealed that LSP1 expression is restricted to tumor infiltrating leukocytes and correlated with BrCa patient outcome (HR = 1.73, p < 0.001). The human BrCa patient-based genomic and proteomic evidence, combined with phenotypic evidence thatLSP1is a negative regulator of leukocyte trafficking, prioritizedLSP1as a novel I-O target. Finally, a novel comparative mapping strategy using mouse genetic linkage revealedTLR1as a plausible therapeutic candidate with strong genomic and phenotypic evidence. Collectively, these data demonstrate a robust and flexible analytical framework for functionally fine-mapping GWAS risk loci to identify the most translatable therapeutic targets for the associated disease.