bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evolutionary ecology of denitrifying methanotrophic NC10 bacteria in the deep‐sea biosphere
Authors: Li Yingdong , Wang Ting , Jing Hongmei , Xiao Yao 
Published: May 2024

AbstractThe NC10 phylum links anaerobic methane oxidation to nitrite denitrification through a unique O2‐producing intra‐aerobic methanotrophic pathway. Although numerous amplicon‐based studies revealed the distribution of this phylum, comprehensive genomic insights and niche characterization in deep‐sea environments were still largely unknown. In this study, we extensively surveyed the NC10 bacteria across diverse deep‐sea environments, including waters, sediments, cold seeps, biofilms, rocky substrates, and subseafloor aquifers. We then reconstructed and analysed 38 metagenome‐assembled genomes (MAGs), and revealed the extensive distribution of NC10 bacteria and their intense selective pressure in these harsh environments. Isotopic analyses combined with gene expression profiling confirmed that active nitrite‐dependent anaerobic methane oxidation (n‐DAMO) occurs within deep‐sea sediments. In addition, the identification of the Wood–Ljungdahl (WL) and 3‐hydroxypropionate/4‐hydroxybutyrat (3HB/4HP) pathways in these MAGs suggests their capability for carbon fixation as chemoautotrophs in these deep‐sea environments. Indeed, we found that for their survival in the oligotrophic deep‐sea biosphere, NC10 bacteria encode two branches of the WL pathway, utilizing acetyl‐CoA from the carbonyl branch for citric acid cycle‐based energy production and methane from the methyl branch for n‐DAMO. The observed low ratios of non‐synonymous substitutions to synonymous substitutions (pN/pS) in n‐DAMO‐related genes across these habitats suggest a pronounced purifying selection that is critical for the survival of NC10 bacteria in oligotrophic deep‐sea environments. These findings not only advance our understanding of the evolutionary adaptations of NC10 bacteria but also underscore the intricate coupling between the carbon and nitrogen cycles within deep‐sea ecosystems, driven by this bacterial phylum.
Redefining the bacteriophage mv4 site‐specific recombination system and the sequence specificity of its attB and core‐attP sites
Authors: Debatisse Kevin , Lopez Pierre , Poli Maryse , Rousseau Philippe , Campos Manuel , Coddeville Michèle , Cocaign‐Bousquet Muriel , Le Bourgeois Pascal 
Published: May 2024

AbstractThrough their involvement in the integration and excision of a large number of mobile genetic elements, such as phages and integrative and conjugative elements (ICEs), site‐specific recombination systems based on heterobivalent tyrosine recombinases play a major role in genome dynamics and evolution. However, despite hundreds of these systems having been identified in genome databases, very few have been described in detail, with none from phages that infect Bacillota (formerly Firmicutes). In this study, we reanalyzed the recombination module of Lactobacillus delbrueckii subsp. bulgaricus phage mv4, previously considered atypical compared with classical systems. Our results reveal that mv4 integrase is a 369 aa protein with all the structural hallmarks of recombinases from the Tn916 family and that it cooperatively interacts with its recombination sites. Using randomized DNA libraries, NGS sequencing, and other molecular approaches, we show that the 21‐bp core‐attP and attB sites have structural similarities to classical systems only if considering the nucleotide degeneracy, with two 7‐bp inverted regions corresponding to mv4Int core‐binding sites surrounding a 7‐bp strand‐exchange region. We also examined the different compositional constraints in the core‐binding regions, which define the sequence space of permissible recombination sites.
A bamboo ‘PeSAPK4‐PeMYB99‐PeTIP4‐3’ regulatory model involved in water transport
Authors: Zhu Chenglei , Lin Zeming , Yang Kebin , Lou Yongfeng , Liu Yan , Li Tiankuo , Li Hui , Di Xiaolin , Wang Jiangfei , Sun Huayu , Li Ying , Li Xueping , Gao Zhimin 
Published: May 2024

Summary

Water plays crucial roles in expeditious growth and osmotic stress of bamboo. Nevertheless, the molecular mechanism of water transport remains unclear.

In this study, an aquaporin gene, PeTIP4‐3, was identified through a joint analysis of root pressure and transcriptomic data in moso bamboo (Phyllostachys edulis). PeTIP4‐3 was highly expressed in shoots, especially in the vascular bundle sheath cells. Overexpression of PeTIP4‐3 could increase drought and salt tolerance in transgenic yeast and rice.

A co‐expression pattern of PeSAPK4, PeMYB99 and PeTIP4‐3 was revealed by WGCNA. PeMYB99 exhibited an ability to independently bind to and activate PeTIP4‐3, which augmented tolerance to drought and salt stress. PeSAPK4 could interact with and phosphorylate PeMYB99 in vivo and in vitro, wherein they synergistically accelerated PeTIP4‐3 transcription. Overexpression of PeMYB99 and PeSAPK4 also conferred drought and salt tolerance in transgenic rice.

Further ABA treatment analysis indicated that PeSAPK4 enhanced water transport in response to stress via ABA signaling. Collectively, an ABA‐mediated cascade of PeSAPK4‐PeMYB99‐PeTIP4‐3 is proposed, which governs water transport in moso bamboo.
Epigenetic regulation of high light‐induced anthocyanin biosynthesis by histone demethylase IBM1 in Arabidopsis
Authors: Fan Di , Wang Xianqiang , Liu Tingting , Liu Huimin , Peng Yingying , Tang Xiaofeng , Ye Xiao , Sun Kuan , Yue Yuchen , Xu Dan , Li Chaofeng , Luo Keming 
Published: May 2024

Summary
In plant species, anthocyanin accumulation is specifically regulated by light signaling. Although the CONSTITUTIVELY PHOTOMORPHOGENIC1/SUPPRESSOR OF PHYA‐105 (COP1/SPA) complex is known to control anthocyanin biosynthesis in response to light, the precise mechanism underlying this process remains largely unknown.
Here, we report that Increase in BONSAI Methylation 1 (IBM1), a JmjC domain‐containing histone demethylase, participates in the regulation of light‐induced anthocyanin biosynthesis in Arabidopsis.
The expression of IBM1 was induced by high light (HL) stress, and loss‐of‐function mutations in IBM1 led to accelerated anthocyanin accumulation under HL conditions. We further identified that IBM1 is directly associated with SPA1/3/4 chromatin in vivo to establish a hypomethylation status on H3K9 and DNA non‐CG at these loci under HL, thereby releasing their expression. Genetic analysis showed that quadruple mutants of IBM1 and SPA1/3/4 resemble spa134 mutants. Overexpression of SPA1 in ibm1 mutants complements the mutant phenotype.
Our results elucidate the significance and mechanism of IBM1 histone demethylase in the epigenetic regulation of anthocyanin biosynthesis in Arabidopsis under HL conditions.
Revisiting the intron hypothesis of QoI resistance in Phyllosticta ampelicida, the causal agent of grape black rot, and other Phyllosticta species
Authors: Horváth Áron N. , Molnár Orsolya , Németh Márk Z. , Pintye Alexandra , Dankó Tamás , Spitzmüller Zsolt , Váczy Zsuzsanna , Váczy Kálmán Z. , Onesti Giovanni , Reis Pedro , Rego Cecilia , Bereczky Zsolt , Kiss Levente , Kovács Gábor M. 
Published: May 2024

AbstractChemical control of grape black rot, caused by Phyllosticta ampelicida, relies mainly on the use of demethylation inhibitors (DMIs) and quinone outside inhibitors (QoIs). The effectiveness of QoI fungicides is influenced by alternative respiration activity, and the exon/intron structure and point mutations in the target protein's gene, the cytochrome b (cytb) gene. Our study aims to investigate the QoI fungicide sensitivity of 48 P. ampelicida isolates in vitro by measuring EC50 and the molecular characteristics of the cytb gene and its mRNA in P. ampelicida and other Phyllosticta species. Mycelial growth tests revealed that the P. ampelicida isolates were sensitive to both azoxystrobin and trifloxystrobin; baseline EC50 values were 0.029 and 0.022 μg/mL, respectively. Addition of salicylhydroxamic acid (SHAM) resulted in lower EC50 values (0.024 and 0.017 μg/mL, respectively). None of the typical point mutations conferring resistance to QoIs in some fungi were detected. A group I intron was present right after the 143rd codon in the cytb gene in four of the six Phyllosticta species examined. The sequence and exon/intron structure of the cytb gene of P. ampelicida isolated from Vitis vinifera is studied in detail and published here. Our results indicate a low risk of QoI resistance development via the G143A mutation in P. ampelicida.
The electrophysiology of sequential adjustments of dual‐task order coordination
Authors: Steinhauser Robert , Steinhauser Marco , Kübler Sebastian , Schubert Torsten , Strobach Tilo 
Published: May 2024

AbstractPerforming two tasks simultaneously involves the coordination of their processing. This task coordination is particularly required in dual‐task situations with varying task orders. When task order switches between subsequent trials, task order coordination leads to task order switch costs in comparison with order repetitions. However, it is open, whether task order coordination is exclusively controlled by the relation of the task orders of the current and the previous trials, or whether additional conditions such as task order before the previous trial leads to a behavioral and neural adjustment of task order coordination. To answer this question, we reanalyzed the data of two previously published experiments with order‐cued dual‐task paradigms. We did so with regard to whether task order switch costs and the EEG component order‐switch positivity in the current dual‐task trial would be modulated by order switches vs. repetitions in the previous trial (Trial N‐1). In Experiment 1, we found a modulation of the task order switch costs in RTs and response reversals; these costs were reduced after an order switch compared with order repetitions in Trial N‐1. In Experiment 2, there were no effects on the task order switch costs in the behavioral data. Nonetheless, we found the order‐switch positivity to be strongly modulated by the order transition of the previous trial in both experiments. The order‐switch positivity was substantially reduced if the previous trial was an order switch (compared to an order repetition) by itself. This implies that order coordination of dual tasks is adjusted in a gradual way depending on trial's history.
Visualising the 2020s UK cost‐of‐living crisis
Authors: Dorling Danny 
Published: May 2024

AbstractThis article is unusual in that it provides a graphical summary of various aspects of the longer‐term crisis that appeared to cumulate in 2022 through to at least early 2024 in terms of especially poor economic and social outcomes for the UK. The article was submitted for consideration in a special issue in the Journal of Social Policy and Administration on diverse perspectives and innovative approaches to addressing the cost of living crisis. This special issues focuses on areas such as financial insecurity, inequalities, food insecurity, food access, policy analysis and the variety of responses there have been. This articles highlights the significant challenges posed by the cost of living crisis in the United Kingdom—the widespread impact on poverty rates, health and well‐being, food insecurity, inequality, and social justice. It does so by presenting a series of images that were mostly produced but not used in print to illustrate the book ‘Shattered Nation’ (Dorling, 2023). These 23 images were not included in the book, but most were posted on the book website. A few are more recent.
Wakanda forever! Consistency in correlates of black nationalist tendencies
Authors: Brown Tony N. , Gorman Quintin , Raynor Autumn , Bento Asia , Culver Julian , Ferguson Jauhara 
Published: May 2024

AbstractObjective:This study investigates correlates of black nationalist tendencies, defined as endorsing sentiments consistent with black nationalism. Black nationalism is an ideology that advocates for cultural, economic, political, and social separatism, and/or community autonomy and self‐reliance as survival tactics. Warrant for this study arises from the opinion black nationalism is an anachronism—a throwback to the 1920s, late 1960s, or early 1990s.Methods:We review correlates from prior studies. Then, using regression models and nationally representative data from black adults participating in the Outlook on Life Surveys, 2012, we address whether those correlates link with black nationalist tendencies today.Results:Few correlates from prior studies predict black nationalist tendencies today. However, correlates such as white antipathy and common fate remain robust predictors. Additionally, views of Barack Obama, whose political ascendency challenges certain tenets of black nationalism, are important correlates.Conclusion:White supremacy makes black nationalism durable and attractive; consequently, certain blacks will always endorse it.
Urban perception by using eye movement data on street view images
Authors: Yang Nai , Deng Zhitao , Hu Fangtai , Chao Yi , Wan Lin , Guan Qingfeng , Wei Zhiwei 
Published: May 2024

AbstractUnderstanding the spatial distribution patterns of urban perception and analyzing the correlation between human emotional perception and street composition elements are important for accurately understanding how people interact with the urban environment, urban planning, and urban management. Previous studies on urban perception using street view data have not fully considered the actual level of attention to different visual elements when browsing street view images. In this article, we use eye tracking technology to collect eye movement data and subjective perception evaluation data when people browse street view images, and analyze the correlation between the time to first fixation, duration of first fixation, and fixation frequency of different visual elements and the six perceptual outcomes of wealthy, safe, lively, beautiful, boring, and depressing. Furthermore, this article integrates eye movement data with street view semantic data and introduces a novel method for predicting urban perception using a machine learning algorithm. The proposed method outperforms a comparative model that solely relies on semantic data, exhibiting higher accuracy in perception prediction. Additionally, the study presents a perceptual mapping of the prediction results, providing a visual representation of the predicted urban perception outcomes. As vision is the primary perceptual channel, this study achieves a more objective and scientifically reliable urban perception, which is of reference value for the study of physical and mental health due to the urban physical environment.
Intra‐ and interobserver agreement in computed tomography localization of primary nonhematopoietic hepatic masses and comparison with surgical and histopathological outcomes in 21 cats
Authors: Bentley Carli , Fouriez‐Lablée Virginie , Rossanese Matteo 
Published: May 2024

AbstractComputed tomography (CT) is commonly used in the staging of hepatic masses and for liver lobectomy planning. Mass location is an important factor in determining the feasibility of resection, including surgical technique and the likelihood of surgical complications. The objectives of this retrospective descriptive cross‐sectional, observer agreement, method comparison study were to assess the reliability of CT in correctly determining the hepatic division and lobar site of origin of feline primary nonhematopoietic hepatic masses, compared with surgically confirmed locations. Furthermore, it provides an overview of the types and locations of liver masses found in a cohort of cats. Pre‐ and postcontrast CT images of 21 cats were independently and simultaneously reviewed by two observers. Intra‐ and interobserver agreements and descriptive statistics on demographic and histological diagnoses were calculated. Based on surgical assessment, it was found that masses most frequently originated from the left hepatic division (13/24, 54%). The most frequent lobar origins were the left lateral (8/24, 33%), left medial (5/24, 21%), and right medial lobes (5/24, 21%). No masses were found originating from the right lateral lobe. CT correctly determined hepatic division and lobar origin in 76% of cases, with good‐to‐excellent intra‐ and interobserver agreement. The hepatic division had higher agreements overall for both observers. Most of the masses were benign (17/21, 81%), and the most prevalent histological diagnoses were biliary cystadenoma (11/21, 52%) and hepatocellular adenoma (6/21, 29%). Findings suggest that postcontrast CT is a reliable method for correctly determining hepatic mass division and lobar origin in cats.
Computed tomographic findings in canine and feline heart base tumors (25 cases)
Authors: Ruiz de Alejos Blanco Laura , Brust Kelsey , Szladovits Balázs , Drees Randi 
Published: May 2024

AbstractTumors located at the heart base are rare in dogs and cats and aortic body tumors (chemodectoma/paraganglioma), hemangiosarcoma, ectopic thyroid carcinoma, lymphoma, and other uncommon neoplasia can be found at that location. The objective of this retrospective case series was to describe the CT characteristics of canine and feline heart base tumors. CT studies of 21 dogs and four cats with histologically or cytologically confirmed heart base tumors were reviewed for size, location, shape, margination, contrast enhancement, adjacent neovascularization, invasion, mass effect, cavitary effusions, and metastasis. Neuroendocrine tumors (15 aortic body tumors, three ectopic thyroid carcinoma, and three nonspecific neuroendocrine) were more commonly observed than hemangiosarcoma (4) and were frequently located between the cranial vena cava and aortic arch (12/21; 57%) and or dorsal to the pulmonary trunk bifurcation/pulmonary arteries (10/21; 48%). Hemangiosarcoma was more commonly found cranioventral to the aortic arch and cranial to the right auricular appendage (3/4; 75%). Mediastinal and peritumoral neovascularization was associated with 16/21 (76%) neuroendocrine tumors but none of the hemangiosarcoma. Median postcontrast attenuation in Hounsfield units (HU) was higher in neuroendocrine (110 HU) than in hemangiosarcoma (51 HU). Pericardial effusion was frequently observed with hemangiosarcoma (3/4; 75%) and infrequently in neuroendocrine (3/21; 14%). In four cases (all neuroendocrine), concurrent cranial mediastinal masses were present. CT provides useful information regarding the characteristics of heart base tumors, indicating differences between the appearance of neuroendocrine tumors and hemangiosarcoma. However, no differences were found between aortic body tumors and ectopic thyroid carcinoma.
Three‐dimensionally printed osteotomy and reaming guides for correction of a multiplanar femoral deformity stabilized with an interlocking nail in a dog
Authors: Scheuermann Logan M. , Kim Stanley E. 
Published: May 2024

AbstractObjectiveTo describe the use of virtual surgical planning (VSP) and three‐dimensionally (3D) printed surgical guides for corrective osteotomies stabilized with an interlocking nail in a dog with a multiplanar femoral deformity.Study designCase report.AnimalsAn 8‐year‐old male neutered mixed breed dog weighing 44 kg.MethodsA dog was presented for a right grade 3 lateral patellar luxation secondary to a multiplanar femoral deformity due to a suspected femoral malunion. A computed tomography (CT) scan was obtained to create virtual femoral models. Corrective osteotomies were simulated with VSP. Custom osteotomy guides and reaming guides were designed to facilitate the correction and the placement of an interlocking nail. The preoperative femoral model, virtually aligned femoral model, custom osteotomy guides, and reaming guides were 3D printed, sterilized, and utilized intraoperatively. A CT scan was performed postoperatively to assess femoral length and alignment.ResultsCustom osteotomy and reaming guides were used as intended by the VSP. Postoperative femoral length as well as frontal, sagittal, and axial plane alignment were within 0.7 mm, 2.2°, 0.5°, and 1.6°, respectively, of the virtually planned femoral model. Two months postoperatively, the dog was sound on visual gait examination, and the patella tracked in the trochlear groove throughout stifle range of motion and was unable to be manually luxated. Radiographs obtained 2 months postoperatively revealed static femoral alignment and implants. Both osteotomies were discernable with callus bridging.ConclusionVirtual surgical planning and custom osteotomy and reaming guides facilitated complex femoral corrective osteotomies and interlocking nail placement.
Human cat borne rabies as the new epidemiology of the disease in the Andes mountains
Authors: Meriño‐Olivella Samir , del Pilar Sánchez‐Bonilla María , Escobar Luis E. , Correa‐Valencia Nathalia M. 
Published: May 2024

AbstractBackgroundRabies virus (RABV) is the etiologic agent of rabies, a fatal brain disease in mammals. Rabies circulation has historically involved the dog has the main source of human rabies worldwide. Nevertheless, in Colombia, cats (Felis catus) have become a relevant species in the epidemiology of rabies.AimsTo characterize rabies cases in humans in Colombia in the last three decades in the context of the epidemiology of the aggressor animal.Materials and MethodsWe conducted a retrospective longitudinal epidemiological study of human rabies caused by cats’ aggression, collecting primary and secondary information. Variables considered included the demography of the patient, symptoms, information about the aggressor animal as the source of infection and the viral variant identified.ResultsWe found that the distribution of rabies incidence over the years has been constant in Colombia. Nevertheless, between 2003 and 2012 a peak of cases occurred in rural Colombia where cats were the most frequent aggressor animal reported. Most cats involved in aggression were unvaccinated against rabies. Cat's clinical signs at the time of the report of the human cases included hypersalivation and changes in behaviour. Human patients were mostly children and female and the exposure primarily corresponded to bite and puncture lacerations in hands. The RABV lineage detected in most cases corresponded to variant 3, linked to the common vampire bat (Desmodus rotundus). The geographical presentation of cat borne RABV in humans occurred along the Andes mountains, epidemiologically known as the rabies red Andean corridor.DiscussionBy finding cats as the primary source of rabies spillover transmission in Colombia, this report highlights the importance of revising national rabies control and prevention protocol in countries in the Andes region.ConclusionOur results demonstrate that rabies vaccination for outdoor cats needs to prioritize to reduce the number of rabies‐related human deaths.