bluuebunny/crossref_metadata_2025_split huggingface dataset:
Malondialdehyde-specific natural IgM inhibit NETosis triggered by culprit site–derived extracellular vesicles from myocardial infarction patients
Authors: Ondracek Anna S , Afonyushkin Taras , Aszlan Adrienne , Taqi Soreen , Koller Thomas , Artner Tyler , Porsch Florentina , Resch Ulrike , Sharma Smriti , Scherz Thomas , Spittler Andreas , Haertinger Maximilian , Hofbauer Thomas M , Ozsvar-Kozma Maria , Seidl Veronika , Beitzke Dietrich , Krueger Marcus , Testori Christoph , Lang Irene M , Binder Christoph J 
Published: August 2024

Abstract

Background and Aims
Neutrophil extracellular traps (NETs) trigger atherothrombosis during acute myocardial infarction (AMI), but mechanisms of induction remain unclear. Levels of extracellular vesicles (EV) carrying oxidation-specific epitopes (OSE), which are targeted by specific natural immunoglobulin M (IgM), are increased at the culprit site in AMI. This study investigated EV as inducers of NETosis and assessed the inhibitory effect of natural anti-OSE–IgM in this process.

Methods
Blood from the culprit and peripheral site of ST-segment elevation myocardial infarction (STEMI) patients (n = 28) was collected, and myocardial function assessed by cardiac magnetic resonance imaging (cMRI) 4 ± 2 days and 195 ± 15 days post-AMI. Extracellular vesicles were isolated from patient plasma and cell culture supernatants for neutrophil stimulation in vitro and in vivo, in the presence of a malondialdehyde (MDA)-specific IgM or an isotype control. NETosis and neutrophil functions were assessed via enzyme-linked immunosorbent assay and fluorescence microscopy. Pharmacological inhibitors were used to map signalling pathways. Neutrophil extracellular trap markers and anti-OSE–IgM were measured by ELISA.

Results
CD45+ MDA+ EV and NET markers were elevated at the culprit site. Extracellular vesicles induced neutrophil activation and NET formation via TLR4 and PAD4, and mice injected with EV showed increased NETosis. Malondialdehyde-specific IgM levels were inversely associated with citH3 in STEMI patient blood. An MDA-specific IgM inhibited EV-induced NET release in vitro and in vivo. CD45+ MDA+ EV concentrations inversely correlated with left ventricular ejection fraction post-AMI.

Conclusions
Culprit site–derived EV induce NETosis, while MDA-specific natural IgM inhibit this effect, potentially impacting outcome after AMI.
Comprehensive analyses of inhibition of the Chinese traditional food-packaging materials, Indocalamus latifolius leaves (Zongye) on Aspergillus flavus
Authors: Peng Wenjing , Ren Xiaoxu , Dai Haiting , Tai Bowen , Yang Bolei , Wang Gang , Li Xu , Xing Fuguo 
Published: August 2024

Abstract

Objectives
The contamination of Aspergillus flavus and aflatoxins (AFs) is one of the most serious safety problems in food and feed. The discovery and application of plant-sourced antifungal agents are hot topics in mycotoxin control. In this study, we aim to develop efficient strategies to control A. flavus and subsequent contamination by AFs.

Materials and Methods
We focused on Zongye essential oil, which was extracted from Indocalamus latifolius leaves (Zongye, the traditional food-packaging materials). Its antifungal and antitoxin activities were observed by volatile test, and the significant morphological and ultrastructural variations were observed by scanning electron microscopy (SEM) and transmission electron microscopy (TEM) analyses. The main components of Zongye essential oil were analyzed by gas chromatography-mass spectrometry (GC-MS). RNA sequencing (RNA-Seq) and real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR) analyses were used to reveal the inhibitory mechanism.

Results
Among them, No. 2 Zongye essential oil completely inhibited the growth and toxin production of A. flavus after 10 µL treatment. Under Zongye essential oil treatment, evidently morphological and ultrastructural variations were observed, such as hyphae shrinkage, partial distortion, and a decrease in conidia number. Longifolene and linalool were the major constituents of Zongye essential oil, accounting for 9.55% and 7.95%, respectively, and linalool had stronger inhibitory effects on fungal growth and mycotoxin biosynthesis than longifolene. Based on the experimental results, the antifungal mechanism was proposed: down-regulations of membrane proteins (AFLA_005560, AFLA_019420, and AFLA_084310, etc.) and conidial genes (fblC, steA, and abaA, etc.) inhibited fungal development, and anti-aflatoxigenic activity might be due to significant down-regulation of AF cluster genes and global regulators (AtfA and AtfB).

Conclusion
A novel antifungal agent, Zongye essential oil, was identified, and its inhibitory mechanism was comprehensively clarified, which is helpful to control AF contamination in an environmentally friendly way.
Finding the missing men with tuberculosis: a participatory approach to identify priority interventions in Uganda
Authors: Nidoi Jasper , Pulford Justin , Wingfield Tom , Rachael Thomson , Ringwald Beate , Katagira Winceslaus , Muttamba Winters , Nattimba Milly , Namuli Zahra , Kirenga Bruce 
Published: August 2024

Abstract
Gender impacts exposure and vulnerability to tuberculosis (TB) evidenced by a higher prevalence of both TB disease and missed TB diagnoses among men, who significantly contribute to new TB infections. We present the formative research phase of a study, which used participatory methods to identify gender-specific interventions for systematic screening of TB among men in Uganda. Health facility-level data were collected at four Ugandan general hospitals (Kawolo, Gombe, Mityana and Nakaseke) among 70 TB stakeholders, including healthcare workers, TB survivors, policymakers and researchers. Using health-seeking pathways, they delineated and compared men’s ideal and actual step-by-step TB health-seeking processes to identify barriers to TB care. The stepping stones method, depicting barriers as a ‘river’ and each ‘steppingstone’ as a solution, was employed to identify interventions which would help link men with TB symptoms to care. These insights were then synthesized in a co-analysis meeting with 17 participants, including representatives from each health facility to develop a consensus on proposed interventions. Data across locations revealed the actual TB care pathway diverted from the ideal pathway due to health system, community, health worker and individual-level barriers such as delayed health seeking, unfavourable facility operating hours and long waiting times that conflicted with men’s work schedules. Stakeholders proposed to address these barriers through the introduction of male-specific services; integrated TB services that prioritize X-ray screening for men with cough; healthcare worker training modules on integrated male-friendly services; training and supporting TB champions to deliver health education to people seeking care; and engagement of private practitioners to screen for TB. In conclusion, our participatory co-design approach facilitated dialogue, learning and consensus between different health actors on context-specific, person-centred TB interventions for men in Uganda. The acceptability, effectiveness and cost effectiveness of the package will now be evaluated in a pilot study.
A telomere-to-telomere gap-free reference genome of Chionanthus retusus provides insights into the molecular mechanism underlying petal shape changes
Authors: Wang Jinnan , Xu Dong , Sang Ya Lin , Sun Maotong , Liu Cuishuang , Niu Muge , Li Ying , Liu Laishuo , Han Xiaojiao , Li Jihong 
Published: August 2024

Abstract
Chionanthus retusus, an arbor tree of the Oleaceae family, is an ecologically and economically valuable ornamental plant for its remarkable adaptability in landscaping. During C. retusus breeding, we observed diverse floral shapes; however, no available genome for C. retusus has hindered the widespread identification of genes related to flower morphology. Thus, a de novo telomere-to-telomere (T2T) gap-free genome was generated. The assembly, incorporating high-coverage and long-read sequencing data, successfully yielded two complete haplotypes (687 and 683 Mb). The genome encompasses 42 864 predicted protein-coding genes, with all 46 telomeres and 23 centromeres in one haplotype. Whole-genome duplication analysis revealed that C. retusus underwent one fewer event of whole-genome duplication after differentiation compared to other species in the Oleaceae family. Furthermore, flower vein diversity was the main reason for the differences in floral shapes. Auxin-related genes were responsible for petal shape formation on genome-based transcriptome analysis. Specifically, the removal and retention of the first intron in CrAUX/IAA20 resulted in the production of two transcripts, and the differences in the expression levels of CrAUX/IAA20 resulted in the variations of flower veins. Compared to transcripts lacking the first intron, transcripts with intron retention caused more severe decreases in the number and length of flower veins in transgenic Arabidopsis thaliana. Our findings will deepen our understanding of flower morphology development and provide important theoretical support for the cultivation of Oleaceae.
A career working on fish
Authors: Vøllestad Leif Asbjørn 
Published: August 2024

Abstract
The fishes are an extremely diverse and interesting group of vertebrates, and provide protein and joy to humans throughout the globe. When I was asked if I could write an essay about my career as a fish ecologist my first thought was: what is there to write about? After some thought I decided to give it a try. I describe how I ended up studying fish and the diversity of fish and topics that I have worked on during my career. My path has included a lot of stochastic events, and I did not have a long-term goal or plan. My road has been a long and winding one, requiring collaboration with people with diverse backgrounds and competences. Teaching and supervision have also been a large part of my career. Many students later became colleagues, and some have become friends. Society and the university have changed over time; I include some comments on university education at the end.
Human-provided food increases aggregation but does not change activity budgets in an urban wading bird
Authors: Wilson Cali A , Hernandez Sonia , Weil Julia N , Ezenwa Vanessa O , Altizer Sonia , Hall Richard J 
Published: August 2024

Abstract
In urban areas, animals often aggregate at higher densities, move less, and alter their diets to consume anthropogenic food, all of which can affect wildlife health and the transmission of infectious diseases. However, it is unknown whether short-term changes in behavior associated with urban resources scale up to more pervasive long-term behavioral changes across landscape types. In this study, we used observational field data to explore how food provisioning affects behaviors relevant to parasite transmission in American white ibis (Eudocimus albus), a waterbird that has recently habituated to urban habitats and anthropogenic food. We found that ibis flock densities more than doubled during short intervals when birds were actively provisioned with food. We then explored activity budgets among urban sites with different levels of provisioning, and found that foraging time decreased with flock size and provisioning levels. Lastly, we compared ibis behavior in more natural wetland sites against urban sites, and found minimal to no differences in behaviors measured here. These results suggest that urbanization and provisioning alter ibis behaviors in ways that could influence, e.g. exposure to parasites in the short-term, but this has not yet resulted in significant long-term changes in activity budgets. Further studies of how urbanization and intentional feeding influences wildlife behavior can inform management strategies to benefit both wildlife and human health.
The SAMI galaxy survey: on the importance of applying multiple selection criteria for finding Milky Way analogues
Authors: Tuntipong Sujeeporn , van de Sande Jesse , Croom Scott M , Barsanti Stefania , Bland-Hawthorn Joss , Brough Sarah , Bryant Julia J , Casura Sarah , Fraser-McKelvie Amelia , Lawrence Jon S , Ristea Andrei , Sweet Sarah M , Zafar Tayyaba 
Published: August 2024

ABSTRACT
Milky Way analogues (MWAs) provide an alternative insight into the various pathways that lead to the formation of disc galaxies with similar properties to the Milky Way (MW). In this study, we explore different selection techniques for identifying MWAs in the Sydney-AAO (Australian Astronomical Observatory) Multi-object Integral field spectrograph (SAMI) Galaxy Survey. We utilize a nearest neighbours method to define MWAs using four selection parameters including stellar mass ($M_{\star }$), star formation rate ($\rm SFR$), bulge-to-total ratio ($B/T$), and disc effective radius ($R_{\rm {e}}$). Based on 15 different selection combinations, we find that including $M_{\star }$ and SFR is essential for minimizing biases in the average MWA properties as compared to the MW. Furthermore, given the MW’s smaller than average size, selection combinations without $R_{\rm {e}}$ result in MWAs being too large. Lastly, we find that $B/T$ is the least important parameter out of the four tested parameters. Using all four selection criteria, we define the top 10 most MW-like galaxies in the GAMA and Cluster regions of the SAMI survey. These most MW-like galaxies are typically barred spirals, with kinematically cold rotating discs and reside in a wide range of environments. Surprisingly, we find no significant differences between the MWAs selected from the GAMA and Cluster regions. Our work highlights the importance of using multiple selection criteria for finding MWAs and also demonstrates potential biases in previous MWA studies.
Exploring the relationship between genetic instability and health outcomes in acute and chronic post-COVID syndrome
Authors: Martins Bruna Alves Alonso , Garcia Ana Leticia Hilario , Borges Malu Siqueira , Picinini Juliana , Serpa Enaile Tuliczewski , Nobles Daiane Dias Ribeiro , Silva Luana Letícia , Dalberto Daiana , Hansen Alana Witt , Spilki Fernando Rosado , Schuler-Faccini Lavínia , Rampelotto Pabulo Henrique , Da Silva Juliana 
Published: August 2024

Abstract
The COVID-19 pandemic has led to the emergence of acute and chronic post-COVID syndromes, which present diverse clinical manifestations. The underlying pathophysiology of these conditions is not yet fully understood, but genetic instability has been proposed as a potential contributing factor. This study aimed to explore the differential impact of physical and psychological health factors on genetic instability in individuals with acute and chronic post-COVID syndromes. In this study, three groups of subjects were analyzed: a control group, an acute post-COVID group, and a chronic post-COVID group, with a total of 231 participants. The participants were assessed using a questionnaire for long-COVID-19COVID, and female participants reported more symptoms than male participants in areas related to fatigue, memory, mental health, and well-being during the chronic phase. Genetic instability was assessed using the comet assay, and participants’ physical and psychological profiles were evaluated. The overall results showed no significant differences in DNA damage, as measured by the comet assay, among the three groups, suggesting that genetic instability, as assessed by this method, may not be a primary driver of the distinct clinical presentations observed in post-COVID syndromes. However, when gender was considered, male participants in the acute long COVID group exhibited higher levels of genetic instability compared to females. Multiple linear regression analysis revealed that gender, age, and waist circumference were significant predictors of DNA damage. Among females in the acute group, sexual health, and eye-related symptoms significantly influenced the increase in DNA damage. These findings indicate the need for further investigation on the gender-specific differences in genetic instability and their potential implications for the pathophysiology of post-COVID syndromes. Exploring alternative markers of genetic instability and the interplay between genetic, inflammatory, and cellular processes could provide valuable insights for the management of these debilitating post-viral sequelae.
Validation of 3D cryoEM single particle reconstruction correctness and handedness with Ewald’s sphere correction
Authors: Bromberg Raquel , Guo Yirui , Borek Dominika , Otwinowski Zbyszek 
Published: August 2024

AbstractThe correct description of quantum scattering places the observed scattering contributions on the Ewald’s sphere and its Friedel mate. In electron microscopy, due to the large radius of the Ewald’s sphere, these contributions are typically merged during data analysis. We present an approach that separates and factorizes these contributions into inversion-symmetric and inversion-antisymmetric components. The correlations between reconstructions derived from these symmetric and antisymmetric components enable the automatic determination of handedness and provide additional validation for the quality of 3D reconstructions. These correlations are robust enough to be routinely used in single-particle reconstructions, even at resolutions below the limit where the curvature of the Ewald’s sphere affects the overall signal-to-noise ratio.SynopsisThe implementation of Ewald’s sphere correction that separates the chirality-sensitive component provides handedness determination and validation of 3D reconstruction.
Identification of the sex determination region and the development of a marker to distinguish males and females in megai abalone (Haliotis gigantea)
Authors: Kina Taito , Hara Motoyuki , Hirase Shotaro , Kikuchi Kiyoshi 
Published: August 2024

AbstractSex identification markers are of considerable value to aquaculture and fisheries as they enable pre-maturity prediction of the genotypic sex of individuals as well as of the sex ratio in offspring. For these reasons, extensive investigations of the mechanisms of sex determination have been conducted in commercially important finfish species, resulting in the development of sex identification markers for many of these. However, research on shellfish is still in its infancy stage. In this study, we investigated the genomic basis of sex determination in megai abalone (Haliotis gigantea), a gastropod species of economic importance in fisheries and aquaculture in East Asia, with the aim of developing a sex identification marker. Initially, we examined the applicability of sex identification markers reported for two otherHaliotisspecies, but found they were not transferable toH. gigantea.We then analyzed the sex chromosomes inH. giganteausing a whole-genome resequencing approach. By calculating the fixation index value between 10 females and 10 males, we identified a genomic region spanning approximately 2 Mb that exhibited nucleotide sequence divergence between the sexes (from the position 260,372 bp to 1,930,278 bp in chromosome 18). This region was located next to the pseudoautosomal region which is characterized by an absence of sequence differentiation between the sexes. In the divergent region, male-specific SNPs were identified but no female-specific SNPs were detected, indicating that this species has an XX-XY sex determination system. By exploring Indel polymorphisms in the divergent region, we successfully developed a codominant PCR marker for sex identification that could be applied to wild individuals from geographically distant locations. A cross-species analysis suggested that the sex determination region inH. giganteawas unlikely to be shared with the closely related speciesH. discus hannai. This raises the possibility of a widespread, rapid turnover of sex chromosomes or sex determination regions in abalones, similar to certain vertebrate lineages such as finfish.
Posterior specification of multi-lineage axial assembloids from human pluripotent stem cells
Authors: Kee N , Leboeuf M , Gómez S , Petitpré C , Mei I , Benlefki S , Hagey D , Dias JM , Lallemend F , EL Andaloussi S , Ericson J , Hedlund E 
Published: August 2024

ABSTRACTElongation of the posterior body axis is driven by multi-potent neuromesodermal progenitors (NMPs), which both self-renew and simultaneously generate neural tube, neural crest, and presomitc mesoderm lineages at successive anterior posterior (A-P) levels. The ensuing diversification of these three NMP lineages is remarkably extensive, and also essential for an immense range of clinically important adult posterior body tissues. Here, we describe a human pluripotent stem cell protocol that successfully specifies authentic NMPs using a cocktail of seven factors (7F). 7F-NMPs express requisite markers, exhibit co-linearHOXactivation, and can be purposely specified into each of the three NMP daughter lineages, demonstrating genuine multi-potency. 3D assembly of neural tube, neural crest, and presomitic mesoderm spheroids followed by long-term floating culture derives mature, multi-compartment Posterior Axial Assembloids, or PAXAs. PAXAs constitute a complex heterogeneous tissue containing spinal motor neurons and interneurons, central and peripheral glia, connective tissues, muscle satellite cells and contractile muscle fibres. Together, 7F-NMP and PAXA protocols establish a versatile in vitro platform to model mechanisms of human posterior body axis development, and for the study of a wide range of human diseases.
Six months of physical inactivity is insufficient to cause chronic kidney disease in C57BL/6J mice
Authors: Opurum Precious C. , Decker Stephen T. , Stuart Deborah , Peterlin Alek D. , Paula Venisia L. , Siripoksup Piyarat , Drummond Micah J. , Sanchez Alejandro , Ramkumar Nirupama , Funai Katsuhiko 
Published: August 2024

AbstractChronic kidney disease (CKD) is a progressive disorder marked by a decline in kidney function. Obesity and sedentary behavior contribute to the development of CKD, though mechanisms by which this occurs are poorly understood. This knowledge gap is worsened by the lack of a reliable murine CKD model that does not rely on injury, toxin, or gene deletion to induce a reduction in kidney function. High-fat diet (HFD) feeding alone is insufficient to cause reduced kidney function until later in life. Here, we employed a small mouse cage (SMC), a recently developed mouse model of sedentariness, to study its effect on kidney function. Wildtype C57BL/6J male mice were housed in sham or SMC housing for six months with HFD in room (22°C) or thermoneutral (30°C) conditions. Despite hyperinsulinemia induced by the SMC+HFD intervention, kidneys from these mice displayed normal glomerular filtration rate (GFR). However, the kidneys showed early signs of kidney injury, including increases in Col1a1 and NGAL transcripts, as well as fibrosis by histology, primarily in the inner medullary/papilla region. High-resolution respirometry and fluorometry experiments showed no statistically significant changes in the capacities for respiration, ATP synthesis, or electron leak. These data confirm the technical challenge in modeling human CKD. They further support the notion that obesity and a sedentary lifestyle make the kidneys more vulnerable, but additional insults are likely required for the pathogenesis of CKD.