bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transposable Element Insertions Are Associated with Batesian Mimicry in the Pantropical Butterfly Hypolimnas misippus
Authors: Orteu Anna , Kucka Marek , Gordon Ian J , Ng’iru Ivy , van der Heijden Eva S M , Talavera Gerard , Warren Ian A , Collins Steve , ffrench-Constant Richard H , Martins Dino J , Chan Yingguang Frank , Jiggins Chris D , Martin Simon H 
Published: February 2024

Abstract
Hypolimnas misippus is a Batesian mimic of the toxic African Queen butterfly (Danaus chrysippus). Female H. misippus butterflies use two major wing patterning loci (M and A) to imitate three color morphs of D. chrysippus found in different regions of Africa. In this study, we examine the evolution of the M locus and identify it as an example of adaptive atavism. This phenomenon involves a morphological reversion to an ancestral character that results in an adaptive phenotype. We show that H. misippus has re-evolved an ancestral wing pattern present in other Hypolimnas species, repurposing it for Batesian mimicry of a D. chrysippus morph. Using haplotagging, a linked-read sequencing technology, and our new analytical tool, Wrath, we discover two large transposable element insertions located at the M locus and establish that these insertions are present in the dominant allele responsible for producing mimetic phenotype. By conducting a comparative analysis involving additional Hypolimnas species, we demonstrate that the dominant allele is derived. This suggests that, in the derived allele, the transposable elements disrupt a cis-regulatory element, leading to the reversion to an ancestral phenotype that is then utilized for Batesian mimicry of a distinct model, a different morph of D. chrysippus. Our findings present a compelling instance of convergent evolution and adaptive atavism, in which the same pattern element has independently evolved multiple times in Hypolimnas butterflies, repeatedly playing a role in Batesian mimicry of diverse model species.
Extracellular vesicle-encapsulated miR-25-3p promotes epithelial–mesenchymal transition and migration of endometrial epithelial cells by inducing macrophage polarization
Authors: Hu Yue , Yuan Ming , Cheng Lei , Xu Le , Wang Guoyun 
Published: February 2024

Abstract
The pathogenesis of adenomyosis is closely related to the epithelial–mesenchymal transition and macrophages. MicroRNAs have been extensively investigated in relation to the epithelial–mesenchymal transition in a range of malignancies. However, there is a paucity of research on extracellular vesicles derived from the eutopic endometrium of adenomyosis and their encapsulated microRNAs. In this study, we investigated the role of microRNA-25-3p derived from extracellular vesicles in inducing macrophage polarization and promoting the epithelial–mesenchymal transition in endometrial epithelial cells of patients with adenomyosis and controls. We obtained eutopic endometrial samples and isolated extracellular vesicles from the culture supernatant of primary endometrial cells. Real-time quantitative PCR analysis demonstrated that microRNA-25-3p was highly expressed in extracellular vesicles, as well as in macrophages stimulated by extracellular vesicles from eutopic endometrium of adenomyosis; and macrophages transfected with microRNA-25-3p exhibited elevated levels of M2 markers, while displaying reduced levels of M1 markers. After co-culture with the above polarized macrophages, endometrial epithelial cells expressed higher levels of N-cadherin and Vimentin, and lower protein levels of E-cadherin and Cytokeratin 7. It was revealed that microRNA-25-3p encapsulated in extracellular vesicles from eutopic endometrial cells could induce macrophage polarization toward M2, and the polarized macrophages promote epithelial–mesenchymal transition in epithelial cells. However, in vitro experiments revealed no significant disparity in the migratory capacity of endometrial epithelial cells between the adenomyosis group and the control group. Furthermore, it was observed that microRNA-25-3p-stimulated polarized macrophages also facilitated the epithelial–mesenchymal transition and migration of endometrial epithelial cells within the control group. Thus, the significance of microRNA-25-3p-induced polarized macrophages in promoting the development of adenomyosis is unclear, and macrophage infiltration alone may be adequate for this process. We emphasize the specificity of the local eutopic endometrial microenvironment and postulate its potential significance in the pathogenesis of adenomyosis.
IgA nephropathy: gut microbiome regulates the production of hypoglycosilated IgA1 via the TLR4 signaling pathway
Authors: Zhu Yifan , He Haidong , Sun Weiqian , Wu Jiajun , Xiao Yong , Peng Yinshun , Hu Ping , Jin Meiping , Liu Ping , Zhang DongLiang , Xie Ting , Huang Lusheng , He Weiming , Wei Minggang , Wang Lishun , Xu Xudong , Tang Yuyan 
Published: February 2024

ABSTRACT

Background
Immunoglobulin A nephropathy (IgAN) is a major cause of primary glomerulonephritis characterized by mesangial deposits of galactose-deficient IgA1 (Gd-IgA1). Toll-like receptors (TLRs), particularly TLR4, are involved in the pathogenesis of IgAN. The role of gut microbiota on IgAN patients was recently investigated. However, whether gut microbial modifications of Gd-IgA1 through TLR4 play a role in IgAN remains unclear.

Methods
We recruited subjects into four groups, including 48 patients with untreated IgAN, 22 treated IgAN patients (IgANIT), 22 primary membranous nephropathy and 31 healthy controls (HCs). Fecal samples were collected to analyze changes in gut microbiome. Gd-IgA1 levels, expression of TLR4, B-cell stimulators and intestinal barrier function were evaluated in all subjects. C57BL/6 mice were treated with a broad-spectrum antibiotic cocktail to deplete the gut microbiota and then gavaged with fecal microbiota transplanted from clinical subjects of every group. Gd-IgA1 and TLR4 pathway were detected in peripheral blood mononuclear cells (PBMCs) from IgAN and HCs co-incubated with lipopolysaccharide (LPS) and TLR4 inhibitor.

Results
Compared with the other three groups, different compositions and decreased diversity demonstrated gut dysbiosis in the untreated IgAN group, especially the enrichment of Escherichia-Shigella. Elevated Gd-IgA1 levels were found in untreated IgAN patients and correlated with gut dysbiosis, TLR4, B-cell stimulators, indexes of intestinal barrier damage and proinflammatory cytokines. In vivo, mice colonized with gut microbiota from IgAN and IgANIT patients mimicked the IgAN phenotype with the activation of TLR4/MyD88/nuclear factor-κB pathway and B-cell stimulators in the intestine, and had with enhanced proinflammatory cytokines. In vitro, LPS activated TLR4/MyD88/NF-κB pathway, B-cell stimulators and proinflammatory cytokines in PBMCs of IgAN patients. This process may induce the overproduction of Gd-IgA1, which was inhibited by TLR4 inhibitors.

Conclusions
Our results illustrated that the gut–kidney axis is involved in the pathogenesis of IgAN. Gut dysbiosis could stimulate the overproduction of Gd-IgA1 via TLR4 signaling pathway production and B-cell stimulators.
Urine cotinine versus self-reported smoking and the risk of chronic kidney disease
Authors: Kunutsor Setor K , Dey Richard S , Touw Daan J , Bakker Stephan J L , Dullaart Robin P F 
Published: February 2024

ABSTRACT

Background and hypothesis
Evidence on the role of smoking in the development of chronic kidney disease (CKD) has mostly relied on self-reported smoking status. We aimed to compare the associations of smoking status as assessed by self-reports and urine cotinine with CKD risk.

Methods
Using the PREVEND prospective study, smoking status was assessed at baseline using self-reports and urine cotinine in 4333 participants (mean age, 52 years) without a history of CKD at baseline. Participants were classified as never, former, light current, and heavy current smokers according to self-reports and comparable cutoffs for urine cotinine. Hazard ratios (HRs) with 95% confidence intervals (CIs) were estimated for CKD.

Results
The percentages of self-reported and cotinine-assessed current smokers were 27.5% and 24.0%, respectively. During a median follow-up of 7.0 years, 593 cases of CKD were recorded. In analyses adjusted for established risk factors, the HRs (95% CI) of CKD for self-reported former, light current, and heavy current smokers compared with never smokers were 1.17 (0.95–1.44), 1.48 (1.10–2.00), and 1.48 (1.14–1.93), respectively. On further adjustment for urinary albumin excretion (UAE), the HRs (95% CI) were 1.07 (0.87–1.32), 1.26 (0.93–1.70), and 1.20 (0.93–1.57), respectively. For urine cotinine-assessed smoking status, the corresponding HRs (95% CI) were 0.81 (0.52–1.25), 1.17 (0.92–1.49), and 1.32 (1.02–1.71), respectively, in analyses adjusted for established risk factors plus UAE.

Conclusion
Self-reported current smoking is associated with increased CKD risk, but dependent on UAE. The association between urine cotinine-assessed current smoking and increased CKD risk is independent of UAE. Urine cotinine-assessed smoking status may be a more reliable risk indicator for CKD incidence than self-reported smoking status.
Three-stage niobium mineralization at Bayan Obo, China
Authors: Yu Yan , Li Yang , Liu Yu , Ling Xiao-Xiao , Wu Li-Guang , Yang Li , Yang Lan , Yang Bo , Zhao Yong-Gang , Li Xian-Hua 
Published: February 2024

ABSTRACT
The Chinese Bayan Obo deposit is a world-class rare earth element (REE) deposit with considerable niobium (Nb) and iron (Fe) resources. A complete genetic understanding on all metals is fundamental for establishing genetic models at Bayan Obo. With extensive research being focused on REE enrichment, the timing and controls of Nb enrichment remain unresolved at Bayan Obo, which is mainly due to the challenges in dating, i.e. multistage thermal events, fine-grained minerals with complex textures and the rare occurrence of uranium-enriched minerals with mature dating methods. Based on robust geological and petrographic frameworks, here we conducted ion probe uranium-lead (U-Pb) dating of ferrocolumbite to unravel the timing, hence the genesis of Nb mineralization. Three types of hydrothermal ferrocolumbites—key Nb-bearing minerals—are identified based on their textures and mineral assemblages. They yield U-Pb ages of 1312 ± 47 Ma (n = 99), 438 ± 7 Ma (n = 93), and 268 ± 5 Ma (n = 19), respectively. In line with deposit geology, we tentatively link the first, second and third stage Nb mineralization to Mesoproterozoic carbonatite magmatism, ubiquitous early Paleozoic hydrothermal activity, and Permian granitic magmatism, respectively. While quantifying the contribution of metal endowment from each stage requires further investigation, our new dates highlight that multi-stage mineralization is critical for Nb enrichment at Bayan Obo, which may also have implications for the enrichment mechanism of Nb in REE deposits in general.
Temperature dependence of spray pyrolysis deposited NiOx layer in inverted perovskite solar cells
Authors: Shibayama Naoyuki , Fukumoto Shota , Kanda Hiroyuki , Shioki Takaya , Fukuda Takeshi , Oka Yoshihiro , Haruyama Yuichi , Suzuki Satoru , Ito Seigo 
Published: February 2024

Abstract
The impact of NiOx layers on the performance of inverted perovskite solar cells (PSCs) has been investigated using multiple analysis methods (thermal gravimetric, differential thermal analysis, X-ray diffraction, X-ray photoelectron spectroscopy, and Soft X-ray photoelectron spectroscopy) of NiOx layers, which were made by spray pyrolysis deposition at different temperatures. The analyses of this study indicate that the efficiency of inverted PSC increases with the Scherrer crystallite size of NiOx. We also observed that the band state of the NiOx layer was changed by Na+ ions migrated from the glass substrate, which also had an impact on the efficiency. The results clearly showed that under high fabrication temperature, migration of matter from the substrate to the hole transport layer affects the electronic structure. Therefore, how these materials are engineered will be important to increase the efficiency of inverted PSCs.
Neuroimmune mechanisms in autism etiology - untangling a complex problem using human cellular models
Authors: Vacharasin Janay M , Ward Joseph A , McCord Mikayla M , Cox Kaitlin , Imitola Jaime , Lizarraga Sofia B 
Published: February 2024

ABSTRACTAutism spectrum disorder (ASD) affects 1 in 36 people and is more often diagnosed in males than in females. Core features of ASD are impaired social interactions, repetitive behaviors and deficits in verbal communication. ASD is a highly heterogeneous and heritable disorder, yet its underlying genetic causes account only for up to 80% of the cases. Hence, a subset of ASD cases could be influenced by environmental risk factors. Maternal immune activation (MIA) is a response to inflammation during pregnancy, which can lead to increased inflammatory signals to the fetus. Inflammatory signals can cross the placenta and blood brain barriers affecting fetal brain development. Epidemiological and animal studies suggest that MIA could contribute to ASD etiology. However, human mechanistic studies have been hindered by a lack of experimental systems that could replicate the impact of MIA during fetal development. Therefore, mechanisms altered by inflammation during human pre-natal brain development, and that could underlie ASD pathogenesis have been largely understudied. The advent of human cellular models with induced pluripotent stem cell (iPSC) and organoid technology is closing this gap in knowledge by providing both access to molecular manipulations and culturing capability of tissue that would be otherwise inaccessible. We present an overview of multiple levels of evidence from clinical, epidemiological, and cellular studies that provide a potential link between higher ASD risk and inflammation. More importantly, we discuss how stem cell-derived models may constitute an ideal experimental system to mechanistically interrogate the effect of inflammation during the early stages of brain development.
The landscape of transcription factor promoter activity during vegetative development in Marchantia
Authors: Romani Facundo , Sauret-Güeto Susanna , Rebmann Marius , Annese Davide , Bonter Ignacy , Tomaselli Marta , Dierschke Tom , Delmans Mihails , Frangedakis Eftychios , Silvestri Linda , Rever Jenna , Bowman John L , Romani Ignacio , Haseloff Jim 
Published: February 2024

Abstract
Transcription factors (TFs) are essential for the regulation of gene expression and cell fate determination. Characterizing the transcriptional activity of TF genes in space and time is a critical step toward understanding complex biological systems. The vegetative gametophyte meristems of bryophytes share some characteristics with the shoot apical meristems of flowering plants. However, the identity and expression profiles of TFs associated with gametophyte organization are largely unknown. With only ∼450 putative TF genes, Marchantia (Marchantia polymorpha) is an outstanding model system for plant systems biology. We have generated a near-complete collection of promoter elements derived from Marchantia TF genes. We experimentally tested reporter fusions for all the TF promoters in the collection and systematically analyzed expression patterns in Marchantia gemmae. This allowed us to build a map of expression domains in early vegetative development and identify a set of TF-derived promoters that are active in the stem-cell zone. The cell markers provide additional tools and insight into the dynamic regulation of the gametophytic meristem and its evolution. In addition, we provide an online database of expression patterns for all promoters in the collection. We expect that these promoter elements will be useful for cell-type-specific expression, synthetic biology applications, and functional genomics.
Determining and weighting effective outputs of humanities research to meet scientific and professional goals: A study of language and literature fields
Authors: Ebrahimi Dorcheh Elahe , Mansouri Ali , Pashootanizadeh Mitra , Mirbagherifard Ali-Asghar , Shabani Ahmad 
Published: February 2024

Abstract
Considering the specific nature of humanities and their fields and the need to design scientific outputs in proportion to these fields, the present study has sought to determine types of scientific outputs in the fields of language and literature and assess their significance and position for the evaluation of research. The study has been conducted in three stages: (1) extracting all the different types of scientific outputs in the fields of language and literature from published articles on the subject, (2) seeking opinions from experts in the fields of language and literature to modify and complete the list of outputs, and (3) Weighing scientific outputs according to the goals and approaches of research. According to the research findings, researchers in the fields of language and literature have generally preferred and prioritized three goals and approaches for their research activities: (1) production of science and promotion of knowledge foundations, (2) applicability and responsiveness to society’s problems, and (3) literary creation/creative literature. Based on the data obtained from the review of documents and interviews, scientific outputs can be divided into two categories of formats and activities. The formats adopted by language and literature researchers to share their results are journal article, book, research project, dissertation/thesis, and conference article. Besides, experts in the fields of language and literature have preferred to do their scientific activities in policy-making, social (media), social (scientific-promotional), and economic contexts. The journal article for the first goal and the book has more weight for the second and third goals. In all three goals, social (media) activities are prioritized.
Estimating Equilibrium in Health Insurance Exchanges: Price Competition and Subsidy Design under the ACA
Authors: Tebaldi Pietro 
Published: February 2024

Abstract
Regulations to design private yet publicly sponsored health insurance markets are increasingly adopted in many OECD countries. Here I combine data and economic theory to analyse the interaction between insurers’ competition and the design of premium subsidies in determining equilibrium outcomes. My empirical model includes adverse selection, rich heterogeneity in preferences for vertically and horizontally differentiated plans and accommodates alternative assumptions on pricing conduct. In the context of the Affordable Care Act in the U.S., I estimate the joint distribution of preferences and expected cost using Californian administrative records on 3.4 million plan choices between 2014 and 2017, combined with plan and survey data on medical claims. An empirical horse race between conduct assumptions favours oligopoly pricing over perfect competition. Considering alternative subsidy designs shows that, in equilibrium, shifting subsidy generosity toward the “young invincibles” would lower premiums for all enrolees while increasing enrolment and profits.
Impact on patient outcomes of spondyloarthritis-inflammatory bowel disease multi-disciplinary meetings
Authors: Sayers Sarah , Lam Danielle , Shah Qutab , Evans Jobie , Parkes Miles , Stober Carmel , Rimmer Joanne , Clunie Gavin , Gudu Tania-Elena , Rosembert Denise , Subramanian Sreedhar , Brookes-Jones Stephanie , Moss Stephen , Raine Tim , Jadon Deepak 
Published: February 2024

Abstract

Objectives
To assess the impact on patient outcomes of the spondyloarthritis (SpA) and inflammatory bowel disease (IBD) multidisciplinary team (MDT) meetings in a large university hospital.

Methods
A single-centre retrospective observational case-note review was conducted assessing the outcome of all 226 cases discussed at the SpA–IBD MDT meetings in a large UK university hospital between 2017 and 2022.

Results
A total of 226 patients were discussed. It was deemed that 97% of MDT meetings helped to improve communication between teams, and 100% were educational. A total of 57% of discussions led to an instant change of disease management, while 40% of discussions resulted in a treatment plan that avoided the use of dual advanced therapy. This improved patient safety by reducing immunosuppression. The MDT meetings were highly cost and time efficient; 125 referrals between specialists were avoided, and in 51 cases there was a significant chance of reducing future drug costs. A timely investigation or appointment was arranged following 50% of MDT discussions, helping to clarify the diagnosis and optimize patient care. Nine percent of meetings enabled drugs to be prescribed to patients that are not yet licensed for the other speciality, thereby improving treatment options available in the management of complex cases.

Conclusion
The MDT meetings have been beneficial for patients, the clinical team and the institution. This approach might be considered by other rheumatology and gastroenterology departments.
Systematic Review and Meta-analysis of Exercise Interventions for Psychotic Disorders: The Impact of Exercise Intensity, Mindfulness Components, and Other Moderators on Symptoms, Functioning, and Cardiometabolic Health
Authors: Rißmayer Matthias , Kambeitz Joseph , Javelle Florian , Lichtenstein Theresa Katharina 
Published: February 2024

Abstract

Background and Hypothesis
Exercise therapy has been shown to be an effective complementary treatment for patients with psychotic disorders. However, the specific impacts of different training modalities remain poorly understood. This article aims to quantitatively review the moderating influence of different exercise modalities, hypothesizing that higher exercise intensity as well as utilization of mindfulness-based exercise (MBE) components, will improve intervention outcomes.

Study Design
PubMed, Web of Science, and PsycINFO were searched from 2010 to March 2022 for randomized controlled trials investigating exercise interventions in patients with psychotic disorders (preregistration: https://doi.org/10.17605/OSF.IO/J8QNS). Outcomes considered were positive/negative symptoms, Positive and Negative Syndrome Scale (PANSS) General Psychopathology/Total scores, depressive symptoms, psychosocial functioning, quality of life, cardiorespiratory fitness, and body mass index. Separate meta-analyses, including moderator analyses, were performed to evaluate the moderating influence of different training modalities.

Study Results
Of 6653 studies, 40 (n = 2111 patients) were included in the meta-analysis. The effects of moderate-intensity exercise exceed low-intensity approaches for PANSS Total scores (P = .02) and depressive symptoms (P = .04). The presence of MBE components was associated with improvements in positive symptoms (P = .04) and PANSS General Psychopathology subscores (P = .04) but also with higher error and between-study heterogeneity. Our analysis also shows improved intervention effects on depression in younger patients (P = .012) and improved psychosocial functioning scores following more frequent sessions (P &lt; .01).

Conclusions
A minimum of moderate intensity should be considered. More frequent training sessions per week also seem to be beneficial. While adding mindfulness elements is promising, it increases heterogeneity and requires caution in terms of generalization.