bluuebunny/crossref_metadata_2025_split huggingface dataset:
The intentionally defective grantor trust: a strategy for Swiss resident US persons engaging in US gift tax exemption planning
Authors: Berlin Matthew , Grisel Guillaume 
Published: September 2024

Abstract
US Persons (including foreign residents) should prepare for the reduction in the US estate and gift tax lifetime exemption scheduled for 2026. A common planning strategy is to set up irrevocable trusts to divest themselves of part of their wealth. However, for US Persons living abroad, a transfer into trust can result in double taxation of income with no treaty relief. An intentionally defective trust can thread this needle, constituting a completed gift for US lifetime exemption purposes while allowing the application of mechanisms to prevent double taxation of income.
Intracorporeal anastomosis versus extracorporeal anastomosis following laparoscopic right hemicolectomy: Surgical outcomes of a single-center observational study
Authors: Elhoofy Ahmed , Nagy Mostafa , Elghandour Abdelrahman M. 
Published: September 2024

Abstract

Background
The Enhanced Recovery After Surgery protocol strongly recommends minimally invasive approach to colon cancer for rapid recovery, lower complication rate, and wound-related complications. Intracorporeal anastomosis (ICA) is believed to offer better patient outcome compared with extracorporeal anastomosis (ECA).

Materials and Methods
From January 2021 to January 2022, a prospective observational study comparing ICA with ECA in patients after elective right hemicolectomy at a local surgical hospital was conducted. We included all patients ≥18 years old who underwent elective right hemicolectomy. Primary outcome was difference in the incidence of surgical site infection and anastomotic leakage postoperatively.

Results
Seventy-one patients had ICA with a mean age of 52 ± 9.8 years, whereas 67 patients had ECA with a mean age 54.2 ± 8.7 years. Mean overall operative time was longer after ICA (169.1 ± 35.7 minutes) compared with the ECA group (147 ± 36.9 minutes), P = 0.0001. Difference in estimated blood loss (P = 0.60), tumor size (P = 0.57), number of excised lymph nodes (P = 0.19), stage (P = 0.66), and pathology of specimen (P = 0.53) between ICA and ECA was nonsignificant. Patients with ICA after right hemicolectomy had a quicker recovery of bowel function and time to pass stool (ICA: 3.74 ± 0.6 days vs ECA: 4 ± 0.5 days, P = 0.009), early commencement of oral intake (ICA: 2.6 ± 1.1 days vs ECA days: 3.6 ± 1.1, P = 0.0001), and fewer days in hospital (ICA: 4.8 ± 1.1 vs ECA: 6.2 ± 1.4, P = 0.0001) compared with patients with ECA, respectively. There were no significant differences in postoperative complications and causes of readmission between the two groups.

Conclusions
ICA offers comparable postoperative complications to ECA but has enhanced patient outcomes in terms of recovery.
Comparative Analysis of Coagulation Activation in Rheumatoid Arthritis Patients Treated With TNF Inhibitors Versus JAK Inhibitors
Authors: Hansildaar Romy , Raadsen Reinder , Gerritsen Martijn , Nagy Magdolna , Dijkshoorn Bas , Spronk H.M.H. , ten Cate Hugo , Nurmohamed M.T. 
Published: September 2024

Objectives
This study aims to investigate the activation of the coagulation system of RA patients and assess changes during anti-inflammatory treatment with tumor necrosis factor blockers (anti-TNF) and Janus kinase inhibitors (JAKi).

Methods
Biomarkers for the coagulation system, including D-dimer, fibrinogen, prothrombin time, activated partial thrombin time, prothrombin fragment 1 + 2, thrombin-antithrombin complex (TAT), activated factor IX, antithrombin complex, and von Willebrand factor (vWF), were longitudinally measured in 83 RA patients treated with anti-TNF and 38 RA patients with JAKi. Data were collected at baseline, after 1, 3, and 6 months.

Results
The mean age was 57 (±14) years; 76% was female. The mean DAS28-CRP was 3.6 (±1.3) for anti-TNF users and 4.1 (±1.4) for JAKi users at baseline and declined in both groups. Baseline coagulation markers levels were comparable between groups. In anti-TNF users, D-dimer and fibrinogen levels significantly declined (−0.31 mg/L, p = 0.01 and −0.71 g/L, p < 0.001, respectively), whereas TAT significantly increased after 6 months follow-up (1.46 μg/L, p = 0.03) and no effect on vWF (p = 0.98). In JAKi users, vWF declined significantly during the 6 months follow-up (−37.41%, p < 0.001); additionally, there were reductions of D-dimer, fibrinogen, and TAT that did not reach significance (−0.17 mg/L, p = 0.59; −0.49 g/L, p = 0.12; and 0.68 μg/L, p = 0.27, respectively).

Conclusions
The prothrombotic tendency in active RA declined during effective treatment with both anti-TNF and JAKi. Altogether, the biomarkers used in this study suggest that an increased VTE risk in the first 6 months due to either treatment with anti-TNF or JAKi is unlikely.
Plant sesquiterpene lactones
Authors: Agatha Olivia , Mutwil-Anderwald Daniela , Tan Jhing Yein , Mutwil Marek 
Published: September 2024

Sesquiterpene lactones (STLs) are a prominent group of plant secondary metabolites predominantly found in the Asteraceae family and have multiple ecological roles and medicinal applications. This review describes the evolutionary and ecological significance of STLs, highlighting their roles in plant defence mechanisms against herbivory and as phytotoxins, alongside their function as environmental signalling molecules. We also cover the substantial role of STLs in medicine and their mode of action in health and disease. We discuss the biosynthetic pathways and the various modifications that make STLs one of the most diverse groups of metabolites. Finally, we discuss methods for identifying and predicting STL biosynthesis pathways.
This article is part of the theme issue ‘The evolution of plant metabolism’.
Evolution of phosphate scouting in the terrestrial biosphere
Authors: Abel Steffen , Naumann Christin 
Published: September 2024

Chemistry assigns phosphorus and its most oxidized form, inorganic phosphate, unique roles for propelling bioenergetics and metabolism in all domains of life, possibly since its very origin on prebiotic Earth. For plants, access to the vital mineral nutrient profoundly affects growth, development and vigour, thus constraining net primary productivity in natural ecosystems and crop production in modern agriculture. Unlike other major biogenic elements, the low abundance and uneven distribution of phosphate in Earth’s crust result from the peculiarities of phosphorus cosmochemistry and geochemistry. Here, we trace the chemical evolution of the element, the geochemical phosphorus cycle and its acceleration during Earth’s history until the present (Anthropocene) as well as during the evolution and rise of terrestrial plants. We highlight the chemical and biological processes of phosphate mobilization and acquisition, first evolved in bacteria, refined in fungi and algae and expanded into powerful phosphate-prospecting strategies during land plant colonization. Furthermore, we review the evolution of the genetic and molecular networks from bacteria to terrestrial plants, which monitor intracellular and extracellular phosphate availabilities and coordinate the appropriate responses and adjustments to fluctuating phosphate supply. Lastly, we discuss the modern global phosphorus cycle deranged by human activity and the challenges imposed ahead.
This article is part of the theme issue ‘Evolution and diversity of plant metabolism’.
Plant terrestrialization: an environmental pull on the evolution of multi-sourced streptophyte phenolics
Authors: Kunz Cäcilia F. , de Vries Sophie , de Vries Jan 
Published: September 2024

Phenolic compounds of land plants are varied: they are chemodiverse, are sourced from different biosynthetic routes and fulfil a broad spectrum of functions that range from signalling phytohormones, to protective shields against stressors, to structural compounds. Their action defines the biology of land plants as we know it. Often, their roles are tied to environmental responses that, however, impacted already the algal progenitors of land plants, streptophyte algae. Indeed, many streptophyte algae successfully dwell in terrestrial habitats and have homologues for enzymatic routes for the production of important phenolic compounds, such as the phenylpropanoid pathway. Here, we synthesize what is known about the production of specialized phenolic compounds across hundreds of millions of years of streptophyte evolution. We propose an evolutionary scenario in which selective pressures borne out of environmental cues shaped the chemodiversity of phenolics in streptophytes.
This article is part of the theme issue ‘The evolution of plant metabolism’.
Understanding metabolic diversification in plants: branchpoints in the evolution of specialized metabolism
Authors: Ji Wenjuan , Osbourn Anne , Liu Zhenhua 
Published: September 2024

Plants are chemical engineers par excellence. Collectively they make a vast array of structurally diverse specialized metabolites. The raw materials for building new pathways (genes encoding biosynthetic enzymes) are commonly recruited directly or indirectly from primary metabolism. Little is known about how new metabolic pathways and networks evolve in plants, or what key nodes contribute to branches that lead to the biosynthesis of diverse chemicals. Here we review the molecular mechanisms underlying the generation of biosynthetic branchpoints. We also consider examples in which new metabolites are formed through the joining of precursor molecules arising from different biosynthetic routes, a scenario that greatly increases both the diversity and complexity of specialized metabolism. Given the emerging importance of metabolic gene clustering in helping to identify new enzymes and pathways, we further cover the significance of biosynthetic gene clusters in relation to metabolic networks and dedicated biosynthetic pathways. In conclusion, an improved understanding of the branchpoints between metabolic pathways will be key in order to be able to predict and illustrate the complex structure of metabolic networks and to better understand the plasticity of plant metabolism.
This article is part of the theme issue ‘The evolution of plant metabolism’.
The evolution of flavonoid biosynthesis
Authors: Davies Kevin M. , Andre Christelle M. , Kulshrestha Samarth , Zhou Yanfei , Schwinn Kathy E. , Albert Nick W. , Chagné David , van Klink John W. , Landi Marco , Bowman John L. 
Published: September 2024

The flavonoid pathway is characteristic of land plants and a central biosynthetic component enabling life in a terrestrial environment. Flavonoids provide tolerance to both abiotic and biotic stresses and facilitate beneficial relationships, such as signalling to symbiont microorganisms, or attracting pollinators and seed dispersal agents. The biosynthetic pathway shows great diversity across species, resulting principally from repeated biosynthetic gene duplication and neofunctionalization events during evolution. Such events may reflect a selection for new flavonoid structures with novel functions that enable occupancy of varied ecological niches. However, the biochemical and genetic diversity of the pathway also likely resulted from evolution along parallel trends across land plant lineages, producing variant compounds with similar biological functions. Analyses of the wide range of whole-plant genome sequences now available, particularly for archegoniate plants, have enabled proposals on which genes were ancestral to land plants and which arose within the land plant lineages. In this review, we discuss the emerging proposals for how the flavonoid pathway may have evolved and diversified.
This article is part of the theme issue ‘The evolution of plant metabolism’.
Biotic interactions, evolutionary forces and the pan-plant specialized metabolism
Authors: de Vries Sophie , Feussner Ivo 
Published: September 2024

Plant specialized metabolism has a complex evolutionary history. Some aspects are conserved across the green lineage, but many metabolites are unique to certain lineages. The network of specialized metabolism continuously diversified, simplified or reshaped during the evolution of streptophytes. Many routes of pan-plant specialized metabolism are involved in plant defence. Biotic interactions are recalled as major drivers of lineage-specific metabolomic diversification. However, the consequences of this diversity of specialized metabolism in the context of plant terrestrialization and land plant diversification into the major lineages of bryophytes, lycophytes, ferns, gymnosperms and angiosperms remain only little explored. Overall, this hampers conclusions on the evolutionary scenarios that shaped specialized metabolism. Recent efforts have brought forth new streptophyte model systems, an increase in genetically accessible species from distinct major plant lineages, and new functional data from a diversity of land plants on specialized metabolic pathways. In this review, we will integrate the recent data on the evolution of the plant immune system with the molecular data of specialized metabolism and its recognition. Based on this we will provide a contextual framework of the pan-plant specialized metabolism, the evolutionary aspects that shape it and the impact on adaptation to the terrestrial environment.
This article is part of the theme issue ‘The evolution of plant metabolism’.
Cytochromes P450 evolution in the plant terrestrialization context
Authors: Werck-Reichhart Danièle , Nelson David R. , Renault Hugues 
Published: September 2024

Plants started to colonize land around 500 million years ago. It meant dealing with new challenges like absence of buoyancy, water and nutrients shortage, increased light radiation, reproduction on land, and interaction with new microorganisms. This obviously required the acquisition of novel functions and metabolic capacities. Cytochrome P450 (CYP) monooxygenases form the largest superfamily of enzymes and are present to catalyse critical and rate-limiting steps in most plant-specific pathways. The different families of CYP enzymes are typically associated with specific functions. CYP family emergence and evolution in the green lineage thus offer the opportunity to obtain a glimpse into the timing of the evolution of the critical functions that were required (or became dispensable) for the plant transition to land. Based on the analysis of currently available genomic data, this review provides an evolutionary history of plant CYPs in the context of plant terrestrialization and describes the associated functions in the different lineages. Without surprise it highlights the relevance of the biosynthesis of antioxidants and UV screens, biopolymers, and critical signalling pathways. It also points to important unsolved questions that would deserve to be answered to improve our understanding of plant adaptation to challenging environments and the management of agricultural traits.
This article is part of the theme issue ‘The evolution of plant metabolism’.
Evolution of small molecule-mediated regulation of arbuscular mycorrhiza symbiosis
Authors: Delaux Pierre-Marc , Gutjahr Caroline 
Published: September 2024

The arbuscular mycorrhizal (AM) symbiosis formed by most extant land plants with symbiotic fungi evolved 450 Ma. AM promotes plant growth by improving mineral nutrient and water uptake, while the symbiotic fungi obtain carbon in return. A number of plant genes regulating the steps leading to an efficient symbiosis have been identified; however, our understanding of the metabolic processes involved in the symbiosis and how they were wired to symbiosis regulation during plant evolution remains limited. Among them, the exchange of chemical signals, the activation of dedicated biosynthesis pathways and the production of secondary metabolites regulating late stages of the AM symbiosis begin to be well described across several land plant clades. Here, we review our current understanding of these processes and propose future directions to fully grasp the phylogenetic distribution and role played by small molecules during this ancient plant symbiosis.
This article is part of the theme issue ‘The evolution of plant metabolism’.
Current and future perspectives for enhancing our understanding of the evolution of plant metabolism
Authors: de Vries Jan , de Vries Sophie , Fernie Alisdair R. 
Published: September 2024

The special issue ‘The evolution of plant metabolism’ has brought together original research, reviews and opinions that cover various aspects from the full breath of plant metabolism including its interaction with the environment including other species. Here, we briefly summarize these efforts and attempts to extract a consensus opinion of the best manner in which to tackle this subject both now and in the future.This article is part of the theme issue ‘The evolution of plant metabolism’.
Cataloguing the postnatal small intestinal transcriptome during the first postnatal month
Authors: Oliveira Luiz Fernando Silva , Khetani Radhika S. , Wu Yu-Syuan , Dasuri Venkata Siva , Harrington Amanda W. , Olaloye Oluwabunmi , Goldsmith Jeffrey , Breault David T. , Konnikova Liza , Ho Sui Shannan J. , O’Connell Amy E. 
Published: September 2024

AbstractIn the first postnatal month, the developing mouse intestine shifts from an immature to a mature intestine that will sustain the organism throughout the lifespan. Here, we surveyed the mouse intestine in C57Bl/6 mice by RNA-Seq to evaluate the changes in gene expression over time from the day of birth through 1 month of age in both the duodenum and ileum. We analyzed gene expression for changes in gene families that correlated with the periods of NEC susceptibility or resistance. We highlight that increased expression of DNA processing genes and vacuolar structure genes, tissue development and morphogenesis genes, and cell migration genes all correlated with NEC susceptibility, while increases in immunity gene sets, intracellular transport genes, ATP production, and intracellular metabolism genes correlated with NEC resistance. Using trends identified in the RNA-Seq analyses, we further evaluated expression of cellular markers and epithelial regulators, immune cell markers, and adenosine metabolism components. We confirmed key changes with qRT-PCR and immunofluorescence. In addition, we compared some findings to humans using human intestinal biopsies and organoids. This dataset can serve as a reference for other groups considering the role of single molecules or molecular families in early intestinal and postnatal development.
PRMT1 Modulates Alternative Splicing to Enhance HPV18 mRNA Stability and Promote the Establishment of Infection
Authors: Williams David E.J. , King Kelly , Jackson Robert , Kuehner Franziska , Arnoldy Christina , Marroquin Jaclyn N. , Tobey Isabelle , Banka Amy , Ragonese Sofia , Van Doorslaer Koenraad 
Published: September 2024

AbstractOnly persistent HPV infections lead to the development of cancer. Thus, understanding the virus-host interplay that influences the establishment of viral infection has important implications for HPV biology and human cancers. The ability of papillomaviruses to establish in cells requires the strict temporal regulation of viral gene expression in sync with cellular differentiation. This control primarily happens at the level of RNA splicing and polyadenylation. However, the details of how this spatio-temporal regulation is achieved still need to be fully understood.Until recently, it has been challenging to study the early events of the HPV lifecycle following infection. We used a single-cell genomics approach to identify cellular factors involved in viral infection and establishment. We identify protein arginine N-methyltransferase 1 (PRMT1) as an important factor in viral infection of primary human cervical cells. PRMT1 is the main cellular enzyme responsible for asymmetric dimethylation of cellular proteins. PRMT1 is an enzyme responsible for catalyzing the methylation of arginine residues on various proteins, which influences processes such as RNA processing, transcriptional regulation, and signal transduction. In this study, we show that HPV18 infection leads to increased PRMT1 levels across the viral lifecycle. PRMT1 is critical for the establishment of a persistent infection in primary cells. Mechanistically, PRMT1 inhibition leads to a highly dysregulated viral splicing pattern. Specifically, reduced PRMT1 activity leads to intron retention and a change in the E6 and E7 expression ratio. In the absence of PRMT1, viral transcripts are destabilized and subject to degradation via the nonsense-mediated decay (NMD) pathway. These findings highlight PRMT1 as a critical regulator of the HPV18 lifecycle, particularly in RNA processing, and position it as a potential therapeutic target for persistent HPV18 infections.
A hierarchical Bayesian model reveals increased precision weighting for afferent cardiac signals, and reduced anxiety, as a function of interoceptive training
Authors: Suksasilp Chatrin , McLanachan Abigail , Quadt Lisa , Boulton Blaise , Mulcahy James , Critchley Hugo D , Smith Ryan , Garfinkel Sarah N 
Published: September 2024

AbstractPerceptual accuracy for interoceptive signals, such as heartbeats, varies in a trait-like manner across individuals and may influence the capacity for emotion regulation and vulnerability to affective symptoms, notably anxiety. Here, we demonstrate that an interoceptive training protocol improved perceptual accuracy in two tasks of heartbeat perception and reduced both state and trait anxiety in a subclinical sample, extending previous findings in autistic adults. Computational modelling indicated that accuracy improvement in the heartbeat discrimination task was associated with increases in the internal reliability estimate for interoceptive signals – their precision weighting – while a lower-level parameter representing noise in the interoceptive signal itself (which influences speed of learning) moderated this precision weighting improvement. Reductions in both state and trait anxiety in the training group were uniquely explained by computational parameter estimates, and not by conventional accuracy measures. These findings indicate that trait-like differences in interoceptive processing are modifiable and can be targeted to alleviate anxiety symptoms, and that interoceptive interventions may be best guided by a computational phenotyping approach.