bluuebunny/crossref_metadata_2025 huggingface dataset:
Positive and Relaxed Selective Pressures Have Both Strongly Influenced the Evolution of Cryonotothenioid Fishes during Their Radiation in the Freezing Southern Ocean
Authors: Bilyk Kevin T , Zhuang Xuan , Papetti Chiara
Published: March 2023

Evolution in the chronic cold of the Southern Ocean has had a profound influence on the physiology of cryonotothenioid fishes. However, the suite of genetic changes underlying the physiological gains and losses in these fishes is still poorly surveyed. By identifying the genomic signatures of selection, this study aims to identify the functional classes of genes that have been changed following two major physiological transitions: the onset of freezing temperatures and the loss of hemoproteins. Looking at the changes that followed the onset of freezing temperatures, positive selective pressure was found among a set of broadly acting gene regulatory factors, suggesting a route through which cryonotothenioid gene expression has been retooled for life in the cold. Further, genes related to the cell cycle and cellular adhesion were found under positive selection suggesting that both present key challenges to life in freezing waters. By contrast, genes showing signatures of the relaxation of selective pressure showed a narrower biological impact, acting on genes related to mitochondrial function. Finally, although chronic cold-water temperatures appear correlated with substantial genetic change, the loss of hemoproteins resulted in little observable change in protein-coding genes relative to their red-blooded relatives. Combined, the influence of positive and relaxed selection shows that long-term exposure to cold has led to profound changes in cryonotothenioid genomes that may make it challenging for them to adapt to a rapidly changing climate.
An unknown essential function of tRNA splicing endonuclease is linked to the integrated stress response and intron debranching
Authors: Hurtig Jennifer E , van Hoof Ambro
Published: March 2023

tRNA splicing endonuclease (TSEN) has a well-characterized role in transfer RNA (tRNA) splicing but also other functions. For yeast TSEN, these other functions include degradation of a subset of mRNAs that encode mitochondrial proteins and an unknown essential function. In this study, we use yeast genetics to characterize the unknown tRNA-independent function(s) of TSEN. Using a high-copy suppressor screen, we found that sen2 mutants can be suppressed by overexpression of SEN54. This effect was seen both for tRNA-dependent and tRNA-independent functions indicating that SEN54 is a general suppressor of sen2, likely through structural stabilization. A spontaneous suppressor screen identified mutations in the intron-debranching enzyme, Dbr1, as tRNA splicing-independent suppressors. Transcriptome analysis showed that sen2 mutation activates the Gcn4 stress response. These Gcn4 target transcripts decreased considerably in the sen2 dbr1 double mutant. We propose that Dbr1 and TSEN may compete for a shared substrate, which TSEN normally processes into an essential RNA, while Dbr1 initiates its degradation. These data provide further insight into the essential function(s) of TSEN. Importantly, single amino acid mutations in TSEN cause the generally fatal neuronal disease pontocerebellar hypoplasia (PCH). The mechanism by which defects in TSEN cause this disease is unknown, and our results reveal new possible mechanisms.
Optimization of solid oxide fuel cell power generation voltage prediction based on improved neural network
Authors: Wei Liming , Wang Yixuan
Published: March 2023

This paper proposes a method for predicting the generation voltage of a solid oxide fuel cell based on the data results of a stand-alone solid oxide fuel single cell simulation model under ideal conditions, with the aim of improving the generation efficiency and extending the service life of the solid oxide fuel cell. In this paper, a modified back propagation (BP) neural network algorithm is used to improve the prediction accuracy of the solid oxide fuel cell generation voltage by using the whale algorithm to optimize the BP neural network model to improve its convergence and achieve the effect of improving the prediction accuracy. First, the characteristics of the independent solid oxide fuel cell are introduced and simulated. Second, the long short-term memory network model, linear regression network model and BP neural network are simulated and compared, and the results show that the BP neural network prediction model is more accurate and can be optimized and improved. Finally, the BP neural network is optimized and simulated using the whale algorithm, and the simulation results show that the method has better convergence and higher prediction accuracy than the traditional BP neural network prediction model.
A Histological and Clinical Study of MatriDerm® Use in Burn Reconstruction
Authors: Dickson Kathryn , Lee Kwang Chear , Abdulsalam Abdulrazak , Amirize Ezekwe , Kankam Hadyn K N , ter Horst Britt , Gardiner Fay , Bamford Amy , Hejmadi Rahul K , Moiemen Naiem
Published: March 2023

Dermal substitutes are well established in the reconstructive ladder. MatriDerm® (Dr. Otto Suwelack Skin & Health Care AG, Billerbeck, Germany) is a single-layer dermal substitute composed of a bovine collagen (type I, III, and V) and elastin hydrolysate, that allows for immediate split-thickness skin grafting (SSG). The aim of this study was to histologically characterize the integration of MatriDerm® when used during burns surgery reconstruction. Eight subjects with nine burn scars and one acute burn wound underwent reconstruction with MatriDerm® and an immediate SSG. MatriDerm® integration and skin graft take were assessed with serial biopsies performed at weeks 1, 2, 3, and 4 and months 2, 3, 6, 9, and 12. Biopsies were assessed with standard special stains and immunohistochemistry, and representative slides were imaged with a transmission electron microscope. Patient satisfaction and clinical scar outcome were assessed with the Vancouver Scar Scale and a patient questionnaire. Histological analysis showed similar stages of wound healing as shown in other dermal templates but on a different timescale. There is early evidence of vascularization and an inflammatory infiltrate in the first 2 weeks. MatriDerm® is resorbed earlier than other dermal substitutes, with evidence of resorption at week 3, to be completely replaced by a neodermis at 2 months. The use of MatriDerm® in reconstruction with immediate skin grafting is supported histologically with early evidence of vascularization to support an epidermal autograft. Future histological studies may help further characterize the ideal dermal substitute.
LAMP Assay as a Rapid Identification Technique of Chinese Citrus Fly and Japanese Orange Fly (Diptera: Tephritidae)
Authors: Yang Wenzhao , Su Yun , Zeng Lingyu , Zhang Yue , Ullah Farman , Wang Xiaoliang , Li Xiaonan , Feng Xiaodong , Li Zhihong
Published: March 2023

Bactrocera tsuneonis and Bactrocera minax are the most destructive pests that damage citrus in China. These key pests hinder the citrus trade, cause significant financial losses, drastically lower citrus production and quality, and decrease farmer enthusiasm for citrus planting. Bactrocera minax and B. tsuneonis are very similar in all life stages. There are limited morphological characteristics to differentiate the adult species, and it is nearly impossible to differentiate these two species in the egg and larval stages. Loop-mediated isothermal amplification (LAMP) is a rapid and robust diagnostic tool used to identify these two species accurately. We designed two sets of primers to distinguish B. minax and B. tsuneonis using DNA barcoding region of the COI gene. Only 50 min was needed under a constant temperature of 65ºC to determine the species of the two flies. The reaction system has high specificity and sensitivity, in which these two species can be accurately distinguished between different geographical populations and 1.0 ng/μL was the lowest DNA concentration that could be detected. Our primers can quickly identify these key pests without knowing their morphology, which could facilitate plant protection workers at the primary level to solve problems in plant quarantine.
A comparison of skin grafts versus local flaps for facial skin cancer from the patient perspective: protocol for a feasibility study
Authors: Huynh Minh N Q , Olaiya Oluwatobi , Kim Patrick J , Gallo Lucas , Dunn Emily , Farrokhyar Forough , McRae Matthew C , Voineskos Sophocles , McRae Mark H
Published: March 2023

Brief abstract

This is a protocol to assess feasibility of conducting a prospective cohort study comparing local flaps versus skin grafts for surgical excision of skin cancer from the face.

Introduction

Skin cancer is the most common malignancy worldwide and the face is one of the most common locations of occurrence. Surgical excision is the most popular treatment for small lesions of the face. Defects can be reconstructed using local flaps or skin grafts. There is a paucity of literature evaluating outcomes after skin cancer surgery from the patient’s perspective using valid measurement tools. The purpose of this study is to assess the feasibility of conducting a prospective observational cohort study. The primary outcomes include recruitment rates, eligibility rate, compliance of intervention and rate of completion of the primary outcome (FACE-Q scales) at 3 months. Secondary outcomes include examining patient characteristic and FACE-Q score differences between local flaps to skin grafts and adverse events.

Methods and analysis

This study is a prospective cohort study consisting of an anticipated 30 patients aged ≥18 years. The study population will consist of a consecutive sample of non-melanoma facial skin cancer patients undergoing a skin graft or local flap. Patients will be followed and evaluated with the FACE-Q questionnaire at 2 weeks, 3 months, 6 months and 1 year post-operation. The following criteria will determine success: patients who meet eligibility criteria >70%; recruitment rate >70%; compliance with intervention >90%; rate of completion of full-scale prospective study primary outcome (FACE-Q at 3 months) >80%; retention rate at 6-month follow-up visit >70%.

Discussion

The findings of this study will be used to guide the sample size calculation for a future, large-scale prospective study.

Trial registration: ClinicalTrials.gov (NCT04842279).
‘What do we talk about when we talk about climate change?’: meaningful environmental education, beyond the info dump
Authors: Campbell Cary
Published: March 2023

Learning about the causes and effects of human-induced climate change is an essential aspect of contemporary environmental education (EE). However, it is increasingly recognized that the familiar ‘information dump delivery mode’ (as Timothy Morton calls it), through which new facts about ecological destruction are being constantly communicated, often contributes to anxiety, cognitive exhaustion, and can ultimately lead to hopelessness and paralysis in the face of ecological issues. In this article, I explore several pathways to approach EE, beyond the presentation and transmission of ecological facts. I position my conceptual discussion around my own teaching experiences speaking about climate change with undergraduate students across several Education classes through 2019 to 2021. I situate these reflections within the current discourse on education and teaching in/for the Anthropocene. Throughout this discussion, I locate various ways in which much EE fails to contribute to student’s agency and empowerment by consistently reducing complex ecological phenomena to a set of problems, mainly economic/technological, to be fixed by technocracy. I propose that a contemplative–existential perspective to EE is capable of responding to these reductions, most basically by providing opportunities and practices for students to process their grief and other emotions through recognizing the Anthropocene as an inescapable reality, but also a reality that cannot be determinately imagined or predicted.
Networks with correlated edge processes
Authors: Süveges Maria , Olhede Sofia Charlotta
Published: March 2023

This article proposes methods to model non-stationary temporal graph processes motivated by a hospital interaction data set. This corresponds to modelling the observation of edge variables indicating interactions between pairs of nodes exhibiting dependence and evolution in time over interactions. This article thus blends (integer) time series models with flexible static network models to produce models of temporal graph data, and statistical fitting procedures for time-varying interaction data. We illustrate the power of our proposed fitting method by analysing a hospital contact network, and this shows the challenge in modelling and inferring correlation between a large number of variables.
Multilevel approach to plant–nanomaterial relationships: from cells to living ecosystems
Authors: Oliveira Halley Caixeta , Seabra Amedea Barozzi , Kondak Selahattin , Adedokun Oluwatosin Peace , Kolbert Zsuzsanna
Published: March 2023

Due to their unique properties, nanomaterials behave peculiarly in biosystems. Regarding plants, the interactions of nanomaterials can be interpreted on a spatial scale: from local interactions in cells to systemic effects on whole plants and on ecosystems. Interpreted on a time scale, the effects of nanomaterials on plants may be immediate or subsequent. At the cellular level, the composition and structure of the cell wall and membranes are modified by nanomaterials, promoting internalization. The effects of nanomaterials on germination and seedling physiology and on the primary and secondary metabolism in the shoot are realized at organ and organism levels. Nanomaterials interact with the beneficial ecological partners of plants. The effects of nanomaterials on plant growth-promoting rhizobacteria and legume–rhizobia symbiosis can be stimulating or inhibitory, depending on the concentration and type of nanomaterial. Nanomaterials exert a negative effect on arbuscular mycorrhiza, and vice versa. Pollinators are exposed to nanomaterials, which may affect plant reproduction. The substances released by the roots influence the availability of nanomaterials in the rhizosphere, and components of plant cells trigger internalization, translocation, and transformation of nanomaterials. Understanding of the multilevel and bidirectional relationship between plants and nanomaterials is of great relevance.
High Nucleotide Diversity Accompanies Differential DNA Methylation in Naturally Diverging Populations
Authors: Ord James , Gossmann Toni I , Adrian-Kalchhauser Irene
Published: March 2023

Epigenetic mechanisms such as DNA methylation (DNAme) are thought to comprise an invaluable adaptive toolkit in the early stages of local adaptation, especially when genetic diversity is constrained. However, the link between genetic diversity and DNAme has been scarcely examined in natural populations, despite its potential to shed light on the evolutionary forces acting on methylation state. Here, we analyzed reduced-representation bisulfite sequencing and whole-genome pool-seq data from marine and freshwater stickleback populations to examine the relationship between DNAme variation (between- and within-population) and nucleotide diversity in the context of freshwater adaptation. We find that sites that are differentially methylated between populations have higher underlying standing genetic variation, with diversity higher among sites that gained methylation in freshwater than those that lost it. Strikingly, although nucleotide diversity is generally lower in the freshwater population as expected from a population bottleneck, this is not the case for sites that lost methylation, which instead have elevated nucleotide diversity in freshwater compared with marine. Subsequently, we show that nucleotide diversity is higher among sites with ancestrally variable methylation and also positively correlates with the sensitivity to environmentally induced methylation change. The results suggest that as selection on the control of methylation state becomes relaxed, so too does selection against mutations at the sites themselves. Increased epigenetic variance in a population is therefore likely to precede genetic diversification.
Transposable Element Interactions Shape the Ecology of the Deer Mouse Genome
Authors: Gozashti Landen , Feschotte Cedric , Hoekstra Hopi E
Published: March 2023

The 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

Aquaporin-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 >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

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

In 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

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

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

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

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

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

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

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

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

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

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

Meiotic 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

Understanding 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

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

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.
Consumers’ willingness to accept gene-edited fruit—An application to quality traits for fresh table grapes
Authors: Uddin Azhar , Gallardo R Karina , Rickard Bradley , Alston Julian , Sambucci Olena
Published: March 2023

Given the increasing number of applications in agriculture of gene editing, specifically CRISPR, it is important to understand consumers’ perceptions of this breeding technology. We estimate consumers’ willingness to pay (WTP) for selected quality attributes of table grapes developed using either conventional breeding or CRISPR. Results show that the willingness-to-pay values for the selected table grape attributes were ranked in the same order for both breeding technologies. We found a slight discount in the overall WTP for table grapes produced using CRISPR compared with conventional breeding, but this discount was neither economically nor statistically significant. Our findings highlight consumers’ preferences for eating-experience attributes—e.g. sweetness and crispness. Results in this study advance the understanding of consumers’ perceptions, contributing to strategies for promoting broader acceptance of CRISPR in the marketplace.
ESTIMATION OF THE GAMMA-RAY FIELD IN AIR FROM RADIOACTIVE SOURCES IN THE GROUND BY NUMERICAL SOLUTION OF THE BOLTZMANN TRANSPORT EQUATION
Authors: Askri Boubaker , Manai Kais , Bouzouita Ahlem , Zaidi Emna , Trabelsi Adel
Published: March 2023

Gamma-ray field in air from radioactive sources uniformly distributed in the ground is calculated by numerically solving the photon transport equation. The scattered flux is developed on the Legendre polynomials basis of the spherical harmonics method and a double P1 approximation is applied. The method is implemented in the Octave programming package. The calculation of the gamma-ray field is also done by Monte Carlo simulation using an optimised geometry model of the soil-air medium that is implemented in Geant4 simulation code. The results obtained by the two methods are in good agreement. The computing time for the spherical harmonics deterministic method is significantly less than the Monte Carlo simulation. Dose rate conversion factors in the air are calculated for the natural radioactive series of 238U and 232Th and for 40K nuclide and for soils contaminated by various radionuclides. The results are in agreement with the published theoretical and experimental studies.
Neural Correlates of Formal Thought Disorder Dimensions in Psychosis
Authors: Maderthaner Lydia , Pavlidou Anastasia , Lefebvre Stephanie , Nadesalingam Niluja , Chapellier Victoria , von Känel Sofie , Kyrou Alexandra , Alexaki Danai , Wüthrich Florian , Weiss Florian , Baumann-Gama Daniel , Wiest Roland , Strik Werner , Kircher Tilo , Walther Sebastian
Published: March 2023

Background and Hypothesis

Formal thought disorder (FTD) is a core symptom of psychosis, but its neural correlates remain poorly understood. This study tested whether four FTD dimensions differ in their association with brain perfusion and brain structure.

Study Design

This cross-sectional study investigated 110 patients with schizophrenia spectrum disorders using 3T magnetic resonance imaging (MRI). The Thought and Language Disorder scale (TALD) was utilized, which comprises four subscales: Objective Positive (OP), Objective Negative (ON), Subjective Positive (SP), and Subjective Negative (SN). Resting-state cerebral blood flow (rsCBF), cortical thickness (CortTh), gray matter volume (GMV), and diffusion MRI tractography were tested for associations with TALD subscales controlling for age, medication, total intracranial volume, and for variance of the 3 other TALD subscales.

Study Results

Following Bonferroni correction, the FTD dimensions presented distinct neural correlates. OP scores were associated with increased rsCBF and increased GMV in the right cerebellum lingual gyrus. Higher SP scores were linked to increased GMV in bilateral prefrontal cortex. In contrast, ON was associated with increased GMV in the right premotor cortex. At more liberal statistical thresholds, higher SP was associated with increased CortTh in the right inferior frontal gyrus, whereas SN scores were linked to decreased GMV in the right prefrontal lobe, the left inferior temporal gyrus, and the left supplementary motor area. Unadjusted analyses mostly corroborated these findings.

Conclusion

These findings stress the heterogeneity in FTD, suggesting distinct neural patterns for specific FTD experiences. In sum, FTD in psychosis may require distinct treatment strategies and further mechanistic investigations on single-item levels.
Active Inference, Epistemic Value, and Uncertainty in Conceptual Disorganization in First-Episode Schizophrenia
Authors: Limongi Roberto , Silva Angelica M , Mackinley Michael , Ford Sabrina D , Palaniyappan Lena
Published: March 2023

Background and Hypothesis

Active inference has become an influential concept in psychopathology. We apply active inference to investigate conceptual disorganization in first-episode schizophrenia. We conceptualize speech production as a decision-making process affected by the latent “conceptual organization”—as a special case of uncertainty about the causes of sensory information. Uncertainty is both minimized via speech production—in which function words index conceptual organization in terms of analytic thinking—and tracked by a domain-general salience network. We hypothesize that analytic thinking depends on conceptual organization. Therefore, conceptual disorganization in schizophrenia would be both indexed by low conceptual organization and reflected in the effective connectivity within the salience network.

Study Design

With 1-minute speech samples from a picture description task and resting state fMRI from 30 patients and 30 healthy subjects, we employed dynamic causal and probabilistic graphical models to investigate if the effective connectivity of the salience network underwrites conceptual organization.

Study Results

Low analytic thinking scores index low conceptual organization which affects diagnostic status. The influence of the anterior insula on the anterior cingulate cortex and the self-inhibition within the anterior cingulate cortex are elevated given low conceptual organization (ie, conceptual disorganization).

Conclusions

Conceptual organization, a construct that explains formal thought disorder, can be modeled in an active inference framework and studied in relation to putative neural substrates of disrupted language in schizophrenia. This provides a critical advance to move away from rating-scale scores to deeper constructs in the pursuit of the pathophysiology of formal thought disorder.