bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transposable Element Interactions Shape the Ecology of the Deer Mouse Genome
Authors: Gozashti Landen , Feschotte Cedric , Hoekstra Hopi E 
Published: March 2023

AbstractThe genomic landscape of transposable elements (TEs) varies dramatically across species, with some TEs demonstrating greater success in colonizing particular lineages than others. In mammals, long interspersed nuclear element (LINE) retrotransposons are typically more common than any other TE. Here, we report an unusual genomic landscape of TEs in the deer mouse, Peromyscus maniculatus. In contrast to other previously examined mammals, long terminal repeat elements occupy more of the deer mouse genome than LINEs (11% and 10%, respectively). This pattern reflects a combination of relatively low LINE activity and a massive invasion of lineage-specific endogenous retroviruses (ERVs). Deer mouse ERVs exhibit diverse origins spanning the retroviral phylogeny suggesting they have been host to a wide range of exogenous retroviruses. Notably, we trace the origin of one ERV lineage, which arose ∼5–18 million years ago, to a close relative of feline leukemia virus, revealing inter-ordinal horizontal transmission. Several lineage-specific ERV subfamilies have very high copy numbers, with the top five most abundant accounting for ∼2% of the genome. We also observe a massive amplification of Kruppel-associated box domain-containing zinc finger genes, which likely control ERV activity and whose expansion may have been facilitated by ectopic recombination between ERVs. Finally, we find evidence that ERVs directly impacted the evolutionary trajectory of LINEs by outcompeting them for genomic sites and frequently disrupting autonomous LINE copies. Together, our results illuminate the genomic ecology that shaped the unique deer mouse TE landscape, shedding light on the evolutionary processes that give rise to variation in mammalian genome structure.
Functional Evolution of Clustered Aquaporin Genes Reveals Insights into the Oceanic Success of Teleost Eggs
Authors: Ferré Alba , Chauvigné François , Vlasova Anna , Norberg Birgitta , Bargelloni Luca , Guigó Roderic , Finn Roderick Nigel , Cerdà Joan 
Published: March 2023

AbstractAquaporin-mediated oocyte hydration is considered important for the evolution of pelagic eggs and the radiative success of marine teleosts. However, the molecular regulatory mechanisms controlling this vital process are not fully understood. Here, we analyzed &gt;400 piscine genomes to uncover a previously unknown teleost-specific aquaporin-1 cluster (TSA1C) comprised of tandemly arranged aqp1aa-aqp1ab2-aqp1ab1 genes. Functional evolutionary analysis of the TSA1C reveals a ∼300-million-year history of downstream aqp1ab-type gene loss, neofunctionalization, and subfunctionalization, but with marine species that spawn highly hydrated pelagic eggs almost exclusively retaining at least one of the downstream paralogs. Unexpectedly, one-third of the modern marine euacanthomorph teleosts selectively retain both aqp1ab-type channels and co-evolved protein kinase-mediated phosphorylation sites in the intracellular subdomains together with teleost-specific Ywhaz-like (14-3-3ζ-like) binding proteins for co-operative membrane trafficking regulation. To understand the selective evolutionary advantages of these mechanisms, we show that a two-step regulated channel shunt avoids competitive occupancy of the same plasma membrane space in the oocyte and accelerates hydration. These data suggest that the evolution of the adaptive molecular regulatory features of the TSA1C facilitated the rise of pelagic eggs and their subsequent geodispersal in the oceanic currents.
Therapeutic Group Singing for Individuals with Parkinson’s Disease: A Conceptual Framework
Authors: Lee Sun Joo , Dvorak Abbey L 
Published: March 2023

Abstract
Parkinson’s disease (PD) is a complex, progressive, and degenerative neurological disorder. With millions affected worldwide, music therapists may have the opportunity to work with individuals with PD and their families. To better understand biological, psychological, and social factors associated with PD, and the interactions between these three systems, researchers encourage a biopsychosocial approach. A biopsychosocial approach supports the idea that biological, psychological, and social systems influence and interact with each other, affecting overall health and quality of life. Music therapy affects biopsychosocial functioning through the use of evidence-based music interventions. One such music therapy intervention supported in the literature for use with individuals with PD and their families is therapeutic group singing. However, this research evidence is diverse and complex. Thus, the purpose of this paper is to present a conceptual framework of the biopsychosocial approach in music therapy focused on therapeutic group singing for individuals with Parkinson’s disease (PD). Our aims include: (1) identifying biopsychosocial (i.e., physical, psychological, and social) factors associated with PD, (2) presenting evidence-based outcomes of therapeutic group singing on biopsychosocial functioning, and (3) crafting a conceptual framework to consolidate evidence about therapeutic group singing as an effective intervention for this population. Research outcomes from various studies demonstrate benefits in biological, psychological, and social functioning from therapeutic group singing interventions. Overall, evidence suggests that therapeutic group singing – as visualized in the conceptual framework – is an effective intervention to address biopsychosocial functioning for individuals with PD and their families.
Wealth, Poverty, Economy
Authors: Blanton Thomas R. 
Published: March 2023

AbstractIn this essay, the usage of the term “economy” is discussed and a working definition proposed; the current state of the discussion of the “ancient economy” in classical studies of Rome is briefly surveyed; and the Synoptic Gospels are situated within that context. Because the terms “wealth” and “poverty” and their Greek and Latin equivalents are imprecise and are used to indicate a wide range of economic situations, this essay utilizes the Friesen-Longenecker economic scale to measure differences in resources attributed to various groups and persons depicted or addressed in the Synoptic Gospels and Q. The Q source presupposes addressees situated slightly lower (i.e., less wealthy) on the economic scale than does the Gospel of Luke, whose addressees are imagined as slightly more affluent. The Gospel of Matthew tends to portray counterfactual economic scenarios in parables that advance theological agendas. The essay identifies issues for further research.
The Child Protection System in India: An Overview
Authors: Bhatt Sanjai , Sanyal Subhashree 
Published: March 2023

Abstract
This chapter provides an overview of the Indian child protection system. As most of India’s development initiatives considers the best interests of children, the country has adopted numerous laws and formulated policies to ensure the protection and improvement of children’s situation. The Juvenile Justice Act is comprehensive legislation focusing on children in need of care and protection, and children in conflict with the law. The chapter also notes how the definition of a child is mostly based on age, which is all people below eighteen years old. Thus, the definition does not refer to the context and experiences associated with childhood, which could be treated as a social construction.
Bible Reading and Interpretation in a Digital Age
Authors: Phillips Peter M. 
Published: March 2023

Abstract
This chapter explores how engagement with the Bible within the prevailing digital culture has been changed through its remediation into digital forms and platforms. The Bible has historically gone through a series of technological shifts—from scrolls to codex to print and now to screens. The chapter explores how these shifts fit into a wider picture of social interaction with the Bible and looks at key texts that have both explored and influenced the remediation processes around Bible reading and interpretation and those concepts which continue to affect remediation within the digital context.
Cosmogenesis and Phonematic Emanation
Authors: Williams Ben 
Published: March 2023

Abstract
After noting the paramount importance placed upon speech and language in the Vedas, Upaniṣads, and philosophy of Bhartṛhari, this chapter charts models of divine sound, word, and phonemes in tantric literature, particularly as the source of all language, mantras, and, in certain sources, reality itself. In surveying numerous tantric scriptures on these themes, including the Niśvāsa corpus, orthodox Śaiva Siddhānta, and traditions devoted to Bhairava and related goddesses, an extraordinary diversity of metaphysical accounts of divine resonance (nāda), phonemes of the syllabary (mātṛkā), and divine speech (parāvāc) surfaces. Whether depicted as condensing into scriptures, languages, or levels of reality, these models of sonic emanation were subjected to the harmonizing agendas of commentators attempting to develop systematic theologies, often in dialogue with the philosophical concerns of non-tantric scholastic traditions. This chapter summarizes both the primary sources and secondary literature on these topics. The latter is briefly evaluated on methodological grounds, noting a desideratum for text-critical scholarship that offers a more global assessment of language and reality in tantric traditions that simultaneously traces shifts in the conceptual and intellectual history of the literature. Numerous passages are cited that highlight views of kuṇḍalinī as a goddess of language related to phonematic emanation, and the current need for a comprehensive study of the early history of this divine power. Another lacuna in secondary scholarship touched upon is the lack of extensive theorization on the sudden preoccupation with script as a new medium for representing tantric deities, mantras, and doctrinal symbols.
Tantric Dimensions of Alchemy
Authors: Sauthoff Patricia 
Published: March 2023

Abstract
This chapter examines the tantric dimensions found within Sanskrit alchemical textual tradition called rasaśāstra. This canon of literature, which dates to the 11th century to today abounds in references to early tantric alchemists, the use of mantra and maṇḍala within alchemical healing practices, and the protection of children from illness caused by demonic possession. The deities of rasaśāstra tend toward the tantric as well, with familiar deities such as Bhairava, Tripurasundarī, and Cāmuṇḍā worshipped during the processing of medical mercurials. This chapter explores the rasaśāstra canon for tantric elements and traces the how the texts combines herbal, metal, mineral, and spiritual medicines to provide a more complete understanding of both healing and religion in the medieval and pre-modern South Asian context.
The Politics of Judicial Impact in Social and Economic Rights Cases
Authors: Botero Sandra , Brinks Daniel M. 
Published: March 2023

Abstract
Can courts advance social and economic rights (SER)? This chapter defines judicial impact and argues that courts produce it by transforming the normative framework and affecting the relationships among actors in three different fields—social, political, and legal—through four different effects—ideational, discursive, organizational, and material. The chapter discusses three differing views of the role of courts in realizing rights in the literature. First, those that argue judicial interventions are counterproductive and may set back the goals SER are ostensibly meant to advance; second, those that view courts as at best irrelevant; and third, those that contend that courts can—under certain conditions—make positive contributions to the goals that SER appear meant to advance. This chapter is squarely in the third camp, arguing that any effectiveness courts can have in advancing SER hinges less on the courts and what they do and more on the politics of impact that follows the courts’ decisions. Impact, according to this chapter, is co-produced by state and social actors working with courts, in a dynamic political process that begins even before a decision is handed down and extends afterward. The concluding section provides examples from the literature to illustrate the different pathways through which courts can affect outcomes.
Social Constitutional Rights and Proportionality
Authors: Alexy Robert 
Published: March 2023

Abstract
The conception of social constitutional rights presented here is based on the principle of human dignity. Human dignity, for its part, comprises all of the elements of the double-triadic concept of person. The double-triadic concept of person includes not only freedom and autonomy but also sentiment. This is to say that the needs of human beings have to be taken seriously. The necessity of social constitutional rights is thereby implied. The definitive content of these rights has to be determined by proportionality analysis, which, in this context, is a matter first and foremost of balancing human dignity and financial possibilities. The right to an existential minimum is a necessary result.
Climatizing Human Rights
Authors: Rodríguez-Garavito César 
Published: March 2023

Abstract
The climate emergency raises the most formidable challenge to economic and social rights (ESRs). The task of urgently advancing climate action through ESRs is what this chapter calls “climatizing” ESRs. There are two complementary routes to climatizing ESRs. The first route involves applying the existing ESR conceptual and legal tools to the climate emergency. This entails both addressing the impacts of global warming on ESRs and ensuring that climate action follows ESR norms. Although much has yet to be done, this chapter shows that human rights actors have made important initial inroads. The second route entails updating ESRs to the Anthropocene’s realities and challenges. This goal requires protecting the planetary boundaries that make life on Earth possible, and thus entails a concern with the limits to human economic activity as well as with the rights of future generations and nonhumans. This chapter theorizes and documents emerging developments in human rights thought and practice that contribute to this goal, including rights-based climate litigation and the recognition of rights of nature.
Dravidian Word Order and the Clausal Peripheries
Authors: Jayaseelan K. A. 
Published: March 2023

Abstract
The word order of the Dravidian languages, customarily described as “free word order,” is strictly determined by clause-internal topic and focus positions within a universal functional architecture that obtains in subject–object–verb (SOV) languages. In terms of these topic/focus positions and using the assumptions of antisymmetry, this chapter explains the intriguing fact that an argument’s placement to the immediate left of the verb (the preferred position of the Dravidian wh-phrase) makes it a focus phrase, while its leftward movement makes it a topic. In clausal complementation, the Dravidian complementiser (which is a quotative, i.e. a “say”-verb) retains its verbal status and hence remains “outside” its complement; it projects its own nonfinite clause that has its own C-domain. Within the determiner phrase, the order of modifiers obeys the Cinque hierarchy.
Indian Gulf Writing
Authors: Karinkurayil Mohamed Shafeeq 
Published: March 2023

Abstract
This chapter surveys Indian Gulf writing, focusing on novels and memoirs in Malayalam and English. The themes discussed are precarity, privation, and humiliation; gender and sexuality; political criticism; and racism. With reference to the Malayalam literary sphere in particular, the chapter demonstrates that migrant literature needs to be studied by taking into account its positionality within the regional field of literary production. Indian Gulf Writing is an area of study with far-reaching implications in fields such as migration literature, petrofiction, and diaspora literature, even as it also offers anthropological insight into the conditions of migrants living in the Persian Gulf.
The Heat Shock Transcription Factor PtHSF1 Mediates Triacylglycerol and Fucoxanthin Synthesis by Regulating the Expression of GPAT3 and DXS in Phaeodactylum tricornutum
Authors: Song Jianquan , Zhao Hejing , Zhang Linxin , Li Zheng , Han Jichang , Zhou Chengxu , Xu Jilin , Li Xiaohui , Yan Xiaojun 
Published: March 2023

Abstract
In addition to being important primary productive forces in marine ecosystems, diatoms are also rich in bioactive substances such as triacylglycerol and fucoxanthin. However, little is known about the transcriptional mechanisms underlying the biosynthesis of these substances. In this study, we found that the heat shock transcription factor PtHSF1 positively regulated the synthesis of triacylglycerol and fucoxanthin in Phaeodactylum tricornutum. Overexpression of PtHSF1 could increase the contents of triacylglycerol and fucoxanthin and upregulate key enzyme genes involved in the triacylglycerol and fucoxanthin biosynthesis pathways. On the other hand, gene silencing of PtHSF1 reduced the contents of triacylglycerol and fucoxanthin and the expression of the key enzyme genes involved in the triacylglycerol and fucoxanthin biosynthesis pathways. Further biochemical analysis revealed that PtHSF1 upregulated glycerol-2-phosphate acyltransferase 3 (GPAT3) and 1-deoxy-d-xylulose 5-phosphate synthase (DXS) by directly binding to their promoters, while genetic analysis demonstrated that PtHSF1 acted upstream of GPAT3 and DXS to regulate triacylglycerol and fucoxanthin synthesis. Therefore, in addition to elucidating the regulation mechanisms underlying PtHSF1-mediated triacylglycerol and fucoxanthin synthesis, this study also provided a candidate target for metabolic engineering of triacylglycerol and fucoxanthin in P. tricornutum.
Reliable genotyping of recombinant genomes using a robust hidden Markov model
Authors: Campos-Martin Rafael , Schmickler Sophia , Goel Manish , Schneeberger Korbinian , Tresch Achim 
Published: March 2023

AbstractMeiotic recombination is an essential mechanism during sexual reproduction and includes the exchange of chromosome segments between homologous chromosomes. New allelic combinations are transmitted to the new generation, introducing novel genetic variation in the offspring genomes. With the improvement of high-throughput whole-genome sequencing technologies, large numbers of recombinant individuals can now be sequenced with low sequencing depth at low costs, necessitating computational methods for reconstructing their haplotypes. The main challenge is the uncertainty in haplotype calling that arises from the low information content of a single genomic position. Straightforward sliding window-based approaches are difficult to tune and fail to place recombination breakpoints precisely. Hidden Markov model (HMM)-based approaches, on the other hand, tend to over-segment the genome. Here, we present RTIGER, an HMM-based model that exploits in a mathematically precise way the fact that true chromosome segments typically have a certain minimum length. We further separate the task of identifying the correct haplotype sequence from the accurate placement of haplotype borders, thereby maximizing the accuracy of border positions. By comparing segmentations based on simulated data with known underlying haplotypes, we highlight the reasons for RTIGER outperforming traditional segmentation approaches. We then analyze the meiotic recombination pattern of segregants of 2 Arabidopsis (Arabidopsis thaliana) accessions and a previously described hyper-recombining mutant. RTIGER is available as an R package with an efficient Julia implementation of the core algorithm.
Physicochemical characterization of porcine respiratory aerosol and considerations for future aerovirology
Authors: Groth Robert , Niazi Sadegh , Spann Kirsten , Johnson Graham R , Ristovski Zoran 
Published: March 2023

AbstractUnderstanding the mechanisms which inactivate airborne viruses is a current challenge. The composition of human respiratory aerosol is poorly understood and needs to be adequately investigated for use in aerovirology studies. Here, the physicochemical properties of porcine respiratory fluid (PRF) from the trachea and lungs were investigated both in bulk solutions and in aerosols. The mass ratio of Na:K in PRF compared with cell culture media (Dulbecco's Modified Eagle Medium, DMEM), which is frequently used in aerovirology studies, was significantly lower (∼2:1 vs ∼16:1). PRF contained significantly more potassium and protein than DMEM. PRF aerosols of all samples were similarly hygroscopic to human respiratory aerosol. PRF particles could nucleate with spatially separated crystals, indicating that the protein matrix was sufficiently viscous to prevent the complete coalescence of aqueous salts prior to efflorescence. The effects of these differences in compositions on the viability of viruses are currently not well understood. The virus suspensions in aerovirology studies need to be reconsidered to adequately reflect a real-world expiration scenario.
Acylated plastoquinone is a novel neutral lipid accumulated in cyanobacteria
Authors: Ishikawa Toshiki , Takano Shunya , Tanikawa Riko , Fujihara Takashi , Atsuzawa Kimie , Kaneko Yasuko , Hihara Yukako 
Published: March 2023

Abstract
Although cyanobacteria do not possess bacterial triacylglycerol (TAG)-synthesizing enzymes, the accumulation of TAGs and/or lipid droplets has been repeatedly reported in a wide range of species. In most cases, the identification of TAG has been based on the detection of the spot showing the mobility similar to the TAG standard in thin-layer chromatography (TLC) of neutral lipids. In this study, we identified monoacyl plastoquinol (acyl PQH) as the predominant molecular species in the TAG-like spot from the unicellular Synechocystis sp. PCC 6803 (S.6803) as well as the filamentous Nostocales sp., Nostoc punctiforme PCC 73102, and Anabaena sp. PCC 7120. In S.6803, the accumulation level of acyl PQH but not TAG was affected by deletion or overexpression of slr2103, indicating that acyl PQH is the physiological product of Slr2103 having homology with the eukaryotic diacylglycerol acyltransferase-2 (DGAT2). Electron microscopy revealed that cyanobacterial strains used in this study do not accumulate lipid droplet structures such as those observed in oleaginous microorganisms. Instead, they accumulate polyhydroxybutyrate (PHB) granules and/or aggregates of alkane, free C16 and C18 saturated fatty acids, and low amounts of TAG in the cytoplasmic area, which can be detected by staining with a fluorescent dye specific to neutral lipids. Unlike these lipophilic materials, acyl PQH is exclusively localized in the membrane fraction. There must be DGAT2-like enzymatic activity esterifying de novo-synthesized C16 and C18 fatty acids to PQH2 in the thylakoid membranes.
Excess Mortality, Sickness and Absence in the Police Workforce in England and Wales During the COVID-19 Pandemic
Authors: Bland Matthew 
Published: March 2023

Abstract
Policing was a critical part of the state response to the COVID-19 pandemic in England and Wales during a period in which the expectations and environment for law enforcement changed rapidly and frequently. While several studies have explored the impact of the pandemic on crime patterns and certain workforce aspects such as leadership and stress, the current study attempts to fill a gap in the literature by quantifiably estimating the impact of the COVID-19 on sickness, absence, and mortality in the police workforce. It finds that while absence rates were higher than normal, this was primarily associated with self-isolation policies. While the incidence of COVID-19 in police officers may have been higher than the incidence in the general public, the mortality rate actually reflected a reduction on the pre-pandemic year. This article discusses the implications for future contingency planning and research.