bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identifying Genomic Regions Targeted During Eggplant Domestication Using Transcriptome Data
Authors: Page Anna M L , Chapman Mark A 
Published: June 2021

AbstractIdentifying genes and traits that have diverged during domestication provides key information of importance for maintaining and even increasing yield and nutrients in existing crops. A “bottom-up” population genetics approach was used to identify signatures of selection across the eggplant genome, to better understand the process of domestication. RNA-seq data were obtained for 4 wild eggplants (Solanum insanum L.) and 16 domesticated eggplants (S. melongena L.) and mapped to the eggplant genome. Single-nucleotide polymorphism (SNPs) exhibiting signatures of selection in domesticates were identified as those exhibiting high FST between the 2 populations (evidence of significant divergence) and low π for the domesticated population (indicative of a selective sweep). Some of these regions appear to overlap with previously identified quantitative trait loci for domestication traits. Genes in regions of linkage disequilibrium surrounding these SNPs were searched against the Arabidopsis thaliana and tomato genomes to find orthologs. Subsequent gene ontology (GO) enrichment analysis identified over-representation of GO terms related to photosynthesis and response to the environment. This work reveals genomic changes involved in eggplant domestication and improvement, and how this compares to observed changes in the tomato genome, revealing shared chromosomal regions involved in the domestication of both species.
Exploitation of ammonia-inducible promoters for enzyme overexpression in Bacillus licheniformis
Authors: Shen Peili , Niu Dandan , Permaul Kugen , Tian Kangming , Singh Suren , Wang Zhengxiang 
Published: June 2021

Abstract
Ammonium hydroxide is conventionally used as an alkaline reagent and cost-effective nitrogen source in enzyme manufacturing processes. However, few ammonia-inducible enzyme expression systems have been described thus far. In this study, genomic-wide transcriptional changes in Bacillus licheniformis CBBD302 cultivated in media supplemented with ammonia were analyzed, resulting in identification of 1443 differently expressed genes, of which 859 genes were upregulated and 584 downregulated. Subsequently, the nucleotide sequences of ammonia-inducible promoters were analyzed and their functionally-mediated expression of amyL, encoding an α-amylase, was shown. TRNA_RS39005 (copA), TRNA_RS41250 (sacA), TRNA_RS23130 (pdpX), TRNA_RS42535 (ald), TRNA_RS31535 (plp), and TRNA_RS23240 (dfp) were selected out of the 859 upregulated genes and each showed higher transcription levels (FPKM values) in the presence of ammonia and glucose than that of the control. The promoters, PcopA from copA, PsacA from sacA, PpdpX from pdpX, Pald from ald, and Pplp from plp, except Pdfp from dfp, were able to mediate amyL expression and were significantly induced by ammonia. The highest enzyme expression level was mediated by Pplp and represented 23% more α-amylase activity after induction by ammonia in a 5-L fermenter. In conclusion, B. licheniformis possesses glucose-independent ammonia-inducible promoters, which can be used to mediate enzyme expression and therefore enhance the enzyme yield in fermentations conventionally fed with ammonia for pH adjustment and nitrogen supply.
Nested sampling with any prior you like
Authors: Alsing Justin , Handley Will 
Published: June 2021

ABSTRACT
Nested sampling is an important tool for conducting Bayesian analysis in Astronomy and other fields, both for sampling complicated posterior distributions for parameter inference, and for computing marginal likelihoods for model comparison. One technical obstacle to using nested sampling in practice is the requirement (for most common implementations) that prior distributions be provided in the form of transformations from the unit hyper-cube to the target prior density. For many applications – particularly when using the posterior from one experiment as the prior for another – such a transformation is not readily available. In this letter, we show that parametric bijectors trained on samples from a desired prior density provide a general purpose method for constructing transformations from the uniform base density to a target prior, enabling the practical use of nested sampling under arbitrary priors. We demonstrate the use of trained bijectors in conjunction with nested sampling on a number of examples from cosmology.
CROssBAR: comprehensive resource of biomedical relations with knowledge graph representations
Authors: Doğan Tunca , Atas Heval , Joshi Vishal , Atakan Ahmet , Rifaioglu Ahmet Sureyya , Nalbat Esra , Nightingale Andrew , Saidi Rabie , Volynkin Vladimir , Zellner Hermann , Cetin-Atalay Rengul , Martin Maria , Atalay Volkan 
Published: June 2021

Abstract
Systemic analysis of available large-scale biological/biomedical data is critical for studying biological mechanisms, and developing novel and effective treatment approaches against diseases. However, different layers of the available data are produced using different technologies and scattered across individual computational resources without any explicit connections to each other, which hinders extensive and integrative multi-omics-based analysis. We aimed to address this issue by developing a new data integration/representation methodology and its application by constructing a biological data resource. CROssBAR is a comprehensive system that integrates large-scale biological/biomedical data from various resources and stores them in a NoSQL database. CROssBAR is enriched with the deep-learning-based prediction of relationships between numerous data entries, which is followed by the rigorous analysis of the enriched data to obtain biologically meaningful modules. These complex sets of entities and relationships are displayed to users via easy-to-interpret, interactive knowledge graphs within an open-access service. CROssBAR knowledge graphs incorporate relevant genes-proteins, molecular interactions, pathways, phenotypes, diseases, as well as known/predicted drugs and bioactive compounds, and they are constructed on-the-fly based on simple non-programmatic user queries. These intensely processed heterogeneous networks are expected to aid systems-level research, especially to infer biological mechanisms in relation to genes, proteins, their ligands, and diseases.
DNA methylation profiling as a model for discovery and precision diagnostics in neuro-oncology
Authors: Pratt Drew , Sahm Felix , Aldape Kenneth 
Published: June 2021

Abstract
Recent years have witnessed a shift to more objective and biologically-driven methods for central nervous system (CNS) tumor classification. The 2016 world health organization (WHO) classification update (“blue book”) introduced molecular diagnostic criteria into the definitions of specific entities as a response to the plethora of evidence that key molecular alterations define distinct tumor types and are clinically meaningful. While in the past such diagnostic alterations included specific mutations, copy number changes, or gene fusions, the emergence of DNA methylation arrays in recent years has similarly resulted in improved diagnostic precision, increased reliability, and has provided an effective framework for the discovery of new tumor types. In many instances, there is an intimate relationship between these mutations/fusions and DNA methylation signatures. The adoption of methylation data into neuro-oncology nosology has been greatly aided by the availability of technology compatible with clinical diagnostics, along with the development of a freely accessible machine learning-based classifier. In this review, we highlight the utility of DNA methylation profiling in CNS tumor classification with a focus on recently described novel and rare tumor types, as well as its contribution to refining existing types.
BOIN: a novel Bayesian design platform to accelerate early phase brain tumor clinical trials
Authors: Yuan Ying , Wu Jing , Gilbert Mark R 
Published: June 2021

AbstractDespite decades of extensive research, the progress in developing effective treatments for primary brain tumors lags behind that of other cancers, largely due to the unique challenges of brain tumors (eg, the blood-brain barrier and high heterogeneity) that limit the delivery and efficacy of many therapeutic agents. One way to address this issue is to employ novel trial designs to better optimize the treatment regimen (eg, dose and schedule) in early phase trials to improve the success rate of subsequent phase III trials. The objective of this article is to introduce Bayesian optimal interval (BOIN) designs as a novel platform to design various types of early phase brain tumor trials, including single-agent and combination regimen trials, trials with late-onset toxicities, and trials aiming to find the optimal biological dose (OBD) based on both toxicity and efficacy. Unlike many novel Bayesian adaptive designs, which are difficult to understand and complicated to implement by clinical investigators, the BOIN designs are self-explanatory and user friendly, yet yield more robust and powerful operating characteristics than conventional designs. We illustrate the BOIN designs using a phase I clinical trial of brain tumor and provide software (freely available at www.trialdesign.org) to facilitate the application of the BOIN design.
Australian Indigenous Ochres
Authors: Huntley Jillian 
Published: June 2021

Abstract
Aboriginal Australians use ochre in varied cultural practices. It is found in the earliest to most recent archaeological sites and geographically across the wide-ranging geological and climatic contexts of the continent. Ochre’s importance in Aboriginal societies, coupled with its availability across Australia and its long-term durability, has led to a ubiquitous archaeological presence with considerable potential to study past cultural landscapes and intergroup interactions, including long-distance trade and exchange. Concentrating on scientific sourcing analyses, this article highlights the benefits of archaeopigment research, defining key terms (ochre, provenience, and provenance) and the technicalities of sourcing studies before discussing theoretical frameworks used in interpretations of ochre distribution patterns. The article argues that as we move away from novel studies on ethnographically well-known source locations into applied research, exceptional Australian records are well placed to investigate territoriality, mobility, intergroup and human–landscape interactions, and to explore the catalysts driving cultural diversity.
Discourses of Disease: The Lifeworld, the Healthworld, and HIV/AIDS
Authors: Higgins Christina 
Published: June 2021

Abstract
Research on HIV/AIDS in linguistics, linguistic anthropology, and literacy studies has followed the course of the pandemic from when it first became widely known in the United States, where early research focused on gay men and their communications with doctors, counselors, and each other in relation to risk and transmission. As time progressed, research shifted to sub-Saharan Africa and South Asia to focus on the discourse of prevention campaigns and public responses to risk reduction strategies. More recently, researchers have examined how people communicate about HIV/AIDS, focusing on how individuals interact with public health discourse in participatory approaches that change the way that HIV/AIDS is framed in educational and institutional contexts. Decades of research has shown a recurring gap in health communication about HIV/AIDS due to the imposition of a biomedical understanding of HIV/AIDS (the “healthworld”) on individuals’ situated perspectives and lived experiences within particular sociocultural contexts (the “lifeworld”).
Reproduction and Language
Authors: Han Sallie 
Published: June 2021

Abstract
The aim of this chapter is to demonstrate the importance and necessity of bringing together the considerations of language and reproduction. While other topics of sexuality have aroused interest in sociolinguistics and linguistic anthropology, the ideas, practices, and experiences of human reproduction, notably pregnancy, remain understudied. At the same time, a discussion of language has been largely absent from the anthropology of reproduction, which has emerged in the last twenty years as an especially vibrant area of cultural and social study. The chapter examines the metaphors and discourses in “talk about” reproduction; the interactions and “talk between” people, like pregnant women and medical health care providers, which shapes the ordinary experiences of reproduction; the “talk to” parties (specifically, fetuses and imagined children) who themselves become constituted through talk; and reproduction as literacy event or one that is mediated and experienced in relation to texts. It is asserted that language is a practice of reproduction.
Resignifications: Linguistic Resistance and Queer Expressions of Latinidad
Authors: Ferrada Juan Sebastian 
Published: June 2021

Abstract
The resignification of language practices among LGBTQIA+ communities has seen the reclamation of terms like queer, dyke, and faggot enter mainstream discourse. Marginalized communities who view the reclamation of language as a form of empowerment also have a long history of resignifying certain forms of pejorative language to revalorize meanings along ethnic and racial lines. This chapter provides an overview of contributions from queer theory, queer studies, and queer linguistics that center the reclamation of historically pejorative terms used for queer communities, but situates these queer resignifications within the context of linguistic reclamations enacted around ethnic and racial affiliations. The chapter specifically focuses on the reclamation of the Spanish terms joto/a/x and jotería by Latinx communities in the United States—terms that have historically been used to denigrate men performing traits associated with femininity—to illustrate how linguistic reclamation provides an avenue for resistance by creating and maintaining new worlds of possibility.
Empire, Postcolonial Criticism, and Biblical Studies
Authors: Jacob Sharon 
Published: June 2021

Abstract
When it comes to the relationship between the Bible and ancient empires, the focus for the most part remains on the past and on the imperial contexts in which these texts were written. It must be noted that even though historical-critical scholarship has drawn our attention to historical contexts, empires continued to remain in the background in biblical studies. This chapter focuses on the relationship between the Bible and empire, not only of the past but also the present. It examines in depth the works of biblical scholars who have made a conscious attempt to expand the field of Biblical studies. Furthermore, by highlighting the points of convergence and divergence between the Bible and precolonial, colonial, and postcolonial empires, scholars can begin to see the ways in which the relationship between the Bible and empire has constantly evolved, transformed, and mutated as scholars transgress boundaries and draw on the work of one another.
The Social Construction of Peace
Authors: Wallis Joanne 
Published: June 2021

Abstract
Peace is socially constructed; it is the product of human agency, and ideas and practices relating to peace are constituted and instantiated within intersubjective social contexts. A constructivist analysis of peace takes a reflexive approach to analyzing peace in order to rethink the tacit ontological assumptions on which dominant international analyses of peace are premised. It suggests that we need to make less certain, more dynamic, contingent, and flexible ontological assumptions regarding how peace is understood and practiced in conflict-affected societies. While acknowledging the ethical issues involved in seeking to know local knowledge, this suggests that we should expand our analysis to consider the everyday lived experiences, beliefs, feelings, ideas, and understandings of those affected by conflict.
Informality in International Political Economy
Authors: Vabulas Felicity 
Published: June 2021

Abstract
Informality is increasingly defining outcomes in an international political economy that has previously been defined by precise treaties and large bureaucracies. Nonetheless, research in the budding area of “informality in IPE” is still nascent. This chapter brings some cohesion to the literature by discussing how soft law, informal governance, and informal intergovernmental organizations are affecting our global economy. By overviewing informality in the areas of international finance, international trade, and international economic institutions, it underscores how important bodies such as the G7, Financial Action Task Force, and Basel Committee are increasingly shaping how states interact. It underscores that informality is neither normatively better nor worse than its formal brethren, but instead that informality will have different effects on international relations. The chapter ends by highlighting ripe areas for more “informality in IPE” research going forward, including a better understanding of how topics such as block chain technologies, informal sanctions, and informal migration affect global politics. Nonetheless, a deeper investigation of these important areas will continue to be challenged by the things that define informality itself—a lack of transparency, working around the rules, and fluidity.
Hedging: Organizational Responses to the Formulation, Implementation, and Enforcement of Government Mandated Changes
Authors: Marcus Alfred , Malen Joel 
Published: June 2021

Abstract
This chapter develops a process model of the hedging behavior of organizations in response to government mandates. To better align the behavior of organizations with the interests of society, governments make many demands on organizations to change their behavior. However, the changes governments require generally do not correspond to the changes organizations want to make, or those that they actually end up making. The process model describes how the variety of external requirements imposed on organizations by government leads to hedging behavior—that is a tendency to simultaneously take actions that align with the regulation while simultaneously taking actions to resist the regulation.
Phosphatidylserine Is Required for the Normal Progression of Cell Plate Formation in Arabidopsis Root Meristems
Authors: Yamaoka Yasuyo , Shin Seungjun , Lee Yuree , Ito Masaki , Lee Youngsook , Nishida Ikuo 
Published: June 2021

Abstract
Phosphatidylserine (PS) is involved in various cellular processes in yeast and animals. However, PS functions in plants remain unclear. In Arabidopsis, PS is relatively enriched in flower and root tissues, and the genetic disturbance of PS biosynthesis in phosphatidylserine synthase1 (PSS1)/ pss1 heterozygotes induces sporophytic and gametophytic defects during pollen maturation. This study functionally characterized PS in Arabidopsis roots and observed that pss1 seedlings exhibited a short-root phenotype by reducing the meristem size and cell elongation capacity. Confocal microscopy imaging analyses of PS with GFP-LactC2 and the endocytic activity with FM 4-64 revealed that although GFP-LactC2 (or PS) was localized in the plasma membrane and endocytic membranes, the lack of PS in pss1 roots did not affect the constitutive endocytosis. Instead, a fluorescence imaging analysis of the cytokinetic phases in the dividing zone of pss1-2 roots revealed a significant delay in telophase progression, requiring active cargo vesicle trafficking for cell plate formation. Confocal microscopy imaging analysis of transgenic GFP-LactC2 root cells with developing cell plates indicated that GFP-LactC2 was localized at the cell plate. Moreover, confocal microscopy images of transgenic pss1-2 and PSS1 roots expressing the cell plate-specific syntaxin construct ProKNOLLE:eGFP-KNOLLE showed abnormal cell plate development in pss1-2ProKNOLLE:eGFP-KNOLLE roots. These results suggested that PS is required for root cytokinesis, possibly because it helps mediate the cargo vesicular trafficking required for cell plate formation.
The metabolomic landscape of rice heterosis highlights pathway biomarkers for predicting complex phenotypes
Authors: Dan Zhiwu , Chen Yunping , Li Hui , Zeng Yafei , Xu Wuwu , Zhao Weibo , He Ruifeng , Huang Wenchao 
Published: June 2021

Abstract
Understanding the molecular mechanisms underlying complex phenotypes requires systematic analyses of complicated metabolic networks and contributes to improvements in the breeding efficiency of staple cereal crops and diagnostic accuracy for human diseases. Here, we selected rice (Oryza sativa) heterosis as a complex phenotype and investigated the mechanisms of both vegetative and reproductive traits using an untargeted metabolomics strategy. Heterosis-associated analytes were identified, and the overlapping analytes were shown to underlie the association patterns for six agronomic traits. The heterosis-associated analytes of four yield components and plant height collectively contributed to yield heterosis, and the degree of contribution differed among the five traits. We performed dysregulated network analyses of the high- and low-better parent heterosis hybrids and found multiple types of metabolic pathways involved in heterosis. The metabolite levels of the significantly enriched pathways (especially those from amino acid and carbohydrate metabolism) were predictive of yield heterosis (area under the curve = 0.907 with 10 features), and the predictability of these pathway biomarkers was validated with hybrids across environments and populations. Our findings elucidate the metabolomic landscape of rice heterosis and highlight the potential application of pathway biomarkers in achieving accurate predictions of complex phenotypes.
Current and emerging biological therapy in adult-onset Still’s disease
Authors: Ma Yuning , Meng Jianfen , Jia Jinchao , Wang Mengyan , Teng Jialin , Zhu Dehao , Yang Chengde , Hu Qiongyi 
Published: June 2021

AbstractAdult-onset Still’s disease (AOSD) is a rare, but characteristic non-familial, multi-genic systemic auto-inflammatory disorder, characterized by high spiking fever, salmon-like evanescent skin rash, polyarthritis, sore throat, hyperferritinemia and leucocytosis. The hallmark of AOSD is a cytokine storm triggered by dysregulation of inflammation. Nowadays, with advances in anti-cytokine biologic agents, the treatment of AOSD is no longer limited to NSAIDs, glucocorticoids or conventional synthetic DMARDs. In this review, we focussed on the roles of these cytokines in the pathogenesis of AOSD and summarized the current and emerging biological therapy.