bluuebunny/crossref_metadata_2025_split huggingface dataset:
SARS-CoV-2 virulence factor ORF3a blocks lysosome function by modulating TBC1D5-dependent Rab7 GTPase cycle
Authors: Walia Kshitiz , Sharma Abhishek , Paul Sankalita , Chouhan Priya , Kumar Gaurav , Ringe Rajesh , Sharma Mahak , Tuli Amit 
Published: March 2024

AbstractSARS-CoV-2, the causative agent of COVID-19, uses the host endolysosomal system for entry, replication, and egress. Previous studies have shown that the SARS-CoV-2 virulence factor ORF3a interacts with the lysosomal tethering factor HOPS complex and blocks HOPS-mediated late endosome and autophagosome fusion with lysosomes. Here, we report that SARS-CoV-2 infection leads to hyperactivation of the late endosomal and lysosomal small GTP-binding protein Rab7, which is dependent on ORF3a expression. We also observed Rab7 hyperactivation in naturally occurring ORF3a variants encoded by distinct SARS-CoV-2 variants. We found that ORF3a, in complex with Vps39, sequesters the Rab7 GAP TBC1D5 and displaces Rab7 from this complex. Thus, ORF3a disrupts the GTP hydrolysis cycle of Rab7, which is beneficial for viral production, whereas the Rab7 GDP-locked mutant strongly reduces viral replication. Hyperactivation of Rab7 in ORF3a-expressing cells impaired CI-M6PR retrieval from late endosomes to the trans-Golgi network, disrupting the biosynthetic transport of newly synthesized hydrolases to lysosomes. Furthermore, the tethering of the Rab7- and Arl8b-positive compartments was strikingly reduced upon ORF3a expression. As SARS-CoV-2 egress requires Arl8b, these findings suggest that ORF3a-mediated hyperactivation of Rab7 serves a multitude of functions, including blocking endolysosome formation, interrupting the transport of lysosomal hydrolases, and promoting viral egress.
A single-cell atlas of Drosophila trachea reveals glycosylation-mediated Notch signaling in cell fate specification
Authors: Li Yue , Lu Tianfeng , Dong Pengzhen , Chen Jian , Zhao Qiang , Wang Yuying , Xiao Tianheng , Wu Honggang , Zhao Quanyi , Huang Hai 
Published: March 2024

AbstractThe Drosophila tracheal system is a favorable model for investigating the program of tubular morphogenesis. This system is established in the embryo by post-mitotic cells, but also undergoes remodeling by adult stem cells. Here, we provide a comprehensive cell atlas of Drosophila trachea using the single-cell RNA-sequencing (scRNA-seq) technique. The atlas documents transcriptional profiles of tracheoblasts within the Drosophila airway, delineating 9 major subtypes. Further evidence gained from in silico as well as genetic investigations highlight a set of transcription factors characterized by their capacity to switch cell fate. Notably, the transcription factors Pebbled, Blistered, Knirps, Spalt and Cut are influenced by Notch signaling and determine tracheal cell identity. Moreover, Notch signaling orchestrates transcriptional activities essential for tracheoblast differentiation and responds to protein glycosylation that is induced by high sugar diet. Therefore, our study yields a single-cell transcriptomic atlas of tracheal development and regeneration, and suggests a glycosylation-responsive Notch signaling in cell fate determination.
Short term supplementation with cranberry extract modulates gut microbiota in human and displays a bifidogenic effect
Authors: Lessard-Lord Jacob , Roussel Charlène , Lupien-Meilleur Joseph , Généreux Pamela , Richard Véronique , Guay Valérie , Roy Denis , Desjardins Yves 
Published: March 2024

AbstractCranberry is associated with multiple health benefits, which are mostly attributed to its high content of (poly)phenols, particularly flavan-3-ols. However, clinical trials attempting to demonstrate these positive effects have yielded heterogeneous results, partly due to the high inter-individual variability associated with gut microbiota interaction with these molecules. In fact, several studies have demonstrated the ability of these molecules to modulate the gut microbiota in animal and in vitro models, but there is a scarcity of information in human subjects. In addition, it has been recently reported that cranberry also contains high concentrations of oligosaccharides, which could contribute to its bioactivity. Hence, the aim of this study was to fully characterize the (poly)phenolic and oligosaccharidic contents of a commercially available cranberry extract and evaluate its capacity to positively modulate the gut microbiota of 28 human subjects. After only four days, the (poly)phenols and oligosaccharides-rich cranberry extract, induced a strong bifidogenic effect, along with an increase in the abundance of several butyrate-producing bacteria, such as Clostridium and Anaerobutyricum. Plasmatic and fecal short-chain fatty acids profiles were also altered by the cranberry extract with a decrease in acetate ratio and an increase in butyrate ratio. Finally, to characterize the inter-individual variability, we stratified the participants according to the alterations observed in the fecal microbiota following supplementation. Interestingly, individuals having a microbiota characterized by the presence of Prevotella benefited from an increase in Faecalibacterium with the cranberry extract supplementation.
Modulating the immune response to SARS-CoV-2 by different nanocarriers delivering an mRNA expressing trimeric RBD of the spike protein: COVARNA Consortium
Authors: Marcos-Villar Laura , Perdiguero Beatriz , Anthiya Shubaash , Borrajo Mireya L. , Lou Gustavo , Franceschini Lorenzo , Esteban Ignasi , Sánchez-Cordón Pedro J. , Zamora Carmen , Sorzano Carlos Óscar S. , Jordá Luis , Codó Laia , Gelpí Josep L. , Sisteré-Oró Marta , Meyerhans Andreas , Thielemans Kris , Martínez-Jiménez Francisco , López-Bigas Núria , García Felipe , Alonso María J. , Plana Montserrat , Esteban Mariano , Gómez Carmen Elena 
Published: March 2024

AbstractVaccines based on mRNA technology have revolutionized the field. In fact, lipid nanoparticles (LNP) formulated with mRNA are the preferential vaccine platform used in the fight against SARS-CoV-2 infection, with wider application against other diseases. The high demand and property right protection of the most potent cationic/ionizable lipids used for LNP formulation of COVID-19 mRNA vaccines have promoted the design of alternative nanocarriers for nucleic acid delivery. In this study we have evaluated the immunogenicity and efficacy of different rationally designed lipid and polymeric-based nanoparticle prototypes against SARS-CoV-2 infection. An mRNA coding for a trimeric soluble form of the receptor binding domain (RBD) of the spike (S) protein from SARS-CoV-2 was encapsulated using different components to form nanoemulsions (NE), nanocapsules (NC) and lipid nanoparticles (LNP). The toxicity and biological activity of these prototypes were evaluated in cultured cells after transfection and in mice following homologous prime/boost immunization. Our findings reveal good levels of RBD protein expression with most of the formulations. In C57BL/6 mice immunized intramuscularly with two doses of formulated RBD-mRNA, the modified lipid nanoparticle (mLNP) and the classical lipid nanoparticle (LNP-1) were the most effective delivery nanocarriers at inducing binding and neutralizing antibodies against SARS-CoV-2. Both prototypes fully protected susceptible K18-hACE2 transgenic mice from morbidity and mortality following a SARS-CoV-2 challenge. These results highlight that modulation of mRNAs immunogenicity can be achieved by using alternative nanocarriers and support further assessment of mLNP and LNP-1 prototypes as delivery vehicles for mRNA vaccines.
Photonic chip-based low-noise microwave oscillator
Authors: Kudelin Igor , Groman William , Ji Qing-Xin , Guo Joel , Kelleher Megan L. , Lee Dahyeon , Nakamura Takuma , McLemore Charles A. , Shirmohammadi Pedram , Hanifi Samin , Cheng Haotian , Jin Naijun , Wu Lue , Halladay Samuel , Luo Yizhi , Dai Zhaowei , Jin Warren , Bai Junwu , Liu Yifan , Zhang Wei , Xiang Chao , Chang Lin , Iltchenko Vladimir , Miller Owen , Matsko Andrey , Bowers Steven M. , Rakich Peter T. , Campbell Joe C. , Bowers John E. , Vahala Kerry J. , Quinlan Franklyn , Diddams Scott A. 
Published: March 2024

AbstractNumerous modern technologies are reliant on the low-phase noise and exquisite timing stability of microwave signals. Substantial progress has been made in the field of microwave photonics, whereby low-noise microwave signals are generated by the down-conversion of ultrastable optical references using a frequency comb1–3. Such systems, however, are constructed with bulk or fibre optics and are difficult to further reduce in size and power consumption. In this work we address this challenge by leveraging advances in integrated photonics to demonstrate low-noise microwave generation via two-point optical frequency division4,5. Narrow-linewidth self-injection-locked integrated lasers6,7 are stabilized to a miniature Fabry–Pérot cavity8, and the frequency gap between the lasers is divided with an efficient dark soliton frequency comb9. The stabilized output of the microcomb is photodetected to produce a microwave signal at 20 GHz with phase noise of −96 dBc Hz−1 at 100 Hz offset frequency that decreases to −135 dBc Hz−1 at 10 kHz offset—values that are unprecedented for an integrated photonic system. All photonic components can be heterogeneously integrated on a single chip, providing a significant advance for the application of photonics to high-precision navigation, communication and timing systems.
Subicular neurons encode concave and convex geometries
Authors: Sun Yanjun , Nitz Douglas A. , Xu Xiangmin , Giocomo Lisa M. 
Published: March 2024

AbstractAnimals in the natural world constantly encounter geometrically complex landscapes. Successful navigation requires that they understand geometric features of these landscapes, including boundaries, landmarks, corners and curved areas, all of which collectively define the geometry of the environment1–12. Crucial to the reconstruction of the geometric layout of natural environments are concave and convex features, such as corners and protrusions. However, the neural substrates that could underlie the perception of concavity and convexity in the environment remain elusive. Here we show that the dorsal subiculum contains neurons that encode corners across environmental geometries in an allocentric reference frame. Using longitudinal calcium imaging in freely behaving mice, we find that corner cells tune their activity to reflect the geometric properties of corners, including corner angles, wall height and the degree of wall intersection. A separate population of subicular neurons encode convex corners of both larger environments and discrete objects. Both corner cells are non-overlapping with the population of subicular neurons that encode environmental boundaries. Furthermore, corner cells that encode concave or convex corners generalize their activity such that they respond, respectively, to concave or convex curvatures within an environment. Together, our findings suggest that the subiculum contains the geometric information needed to reconstruct the shape and layout of naturalistic spatial environments.
Harmonised statistics and maps of forest biomass and increment in Europe
Authors: Avitabile Valerio , Pilli Roberto , Migliavacca Mirco , Duveiller Gregory , Camia Andrea , Blujdea Viorel , Adolt Radim , Alberdi Iciar , Barreiro Susana , Bender Susann , Borota Dragan , Bosela Michal , Bouriaud Olivier , Breidenbach Johannes , Cañellas Isabel , Čavlović Jura , Colin Antoine , Di Cosmo Lucio , Donis Janis , Fischer Christoph , Freudenschuss Alexandra , Fridman Jonas , Gasparini Patrizia , Gschwantner Thomas , Hernández Laura , Korhonen Kari , Kulbokas Gintaras , Kvist Vivian , Latte Nicolas , Lazdins Andis , Lejeune Philippe , Makovskis Kristaps , Marin Gheorghe , Maslo Jan , Michorczyk Artur , Mionskowski Marcin , Morneau François , Myszkowski Marcin , Nagy Kinga , Nilsson Mats , Nord-Larsen Thomas , Pantic Damjan , Perin Jerôme , Redmond John , Rizzo Maria , Šebeň Vladimír , Skudnik Mitja , Snorrason Arnor , Sroga Radosław , Stoyanov Todor , Svensson Arvid , Talarczyk Andrzej , Teeuwen Sander , Thürig Esther , Uva José , Mubareka Sarah 
Published: March 2024

AbstractForest biomass is an essential resource in relation to the green transition and its assessment is key for the sustainable management of forest resources. Here, we present a forest biomass dataset for Europe based on the best available inventory and satellite data, with a higher level of harmonisation and spatial resolution than other existing data. This database provides statistics and maps of the forest area, biomass stock and their share available for wood supply in the year 2020, and statistics on gross and net volume increment in 2010–2020, for 38 European countries. The statistics of most countries are available at a sub-national scale and are derived from National Forest Inventory data, harmonised using common reference definitions and estimation methodology, and updated to a common year using a modelling approach. For those counties without harmonised statistics, data were derived from the State of Europe’s Forest 2020 Report at the national scale. The maps are coherent with the statistics and depict the spatial distribution of the forest variables at 100 m resolution.
Selection of social comparison standards in cardiac patients with and without experienced defibrillator shock
Authors: Willy Kevin , Meyer Thomas , Eckardt Lars , Morina Nexhmedin 
Published: March 2024

AbstractPatients with an implantable cardioverter-defibrillator (ICD) often report psychological distress. Literature suggests that patients with physical disease often compare their well-being and coping to fellow patients. However, we lack knowledge on social comparison among patients with ICD. In this study, we examined psychological distress and social comparison selection in patients with (ICD+) and without experienced ICD shocks (ICD−). We theorized that relative to ICD− patients, those with ICD+ display higher levels of psychological distress and thereby compare more frequently with fellow patients with more severe disease, but better disease coping and try to identify more strongly with these standards to improve their own coping. We recruited 92 patients with (ICD+, n = 38) and without an experienced ICD shock (ICD−, n = 54), who selected one of four comparison standards varying in disease severity and coping capacity. Relative to ICD−, ICD+ patients reported higher levels of device-related distress, but there were no significant differences in anxiety, depression, or quality of life. ICD+ patients selected more often comparison standards with poor coping and, irrespective of standard choice, displayed more negative mood following comparison. Our results show that ICD+ patients tend to perform unfavorable comparisons to fellow patients, which might explain higher psychological distress and worse coping. These findings warrant further research into social comparison as a relevant coping mechanism in ICD patients.
Hydrodynamic features of pulsed solvent extractor for separation of two metals by using the antagonistic effect of solvents
Authors: Asadollahzadeh Mehdi , Torkaman Rezvan 
Published: March 2024

AbstractSeparating copper and cobalt ions is crucial due to the industry’s strategic reliance on both these elements. When the extraction process is able to significantly increase the separation factor, it becomes favorable to separate two ions. However, the presence of Cu(II) ions together with Co(II) hinders the achievement of optimum efficiency when using commonly available extractants. This study conducted the separation of the two elements using both batch and continuous methods in a pilot plant pulsed column equipped with a disc and doughnut structure. The initial step involved optimizing the key variables to maximize the separation factor using the central composite design procedure. The optimization of Cyanex272, Cyphos IL 101 concentrations, and the pH value of the aqueous phase were all adjusted to 0.024 M, 0.046 M, and 7.3, correspondingly. In the following step, the hydrodynamic characteristics and extraction performance were examined in the pulsed column of the pilot plant. The findings indicated that the presence of Cyphos IL 101 resulted in an increased separation factor and efficiency within the column. As a result, the ionic liquid enhances performance without encountering any operational issues. This additive is considered an environmentally friendly solvent and does not cause any negative impacts. Consequently, it is suggested for utilization in continuous industrial processes.
Experimental and numerical investigation of the mechanical properties and energy evolution of sandstone–concrete combined body
Authors: Yuan Shisong , Du Bin , Shen Mingxuan 
Published: March 2024

AbstractStudying the mechanical properties of rock–concrete combined body is crucial to ensure the safety and stability of engineering structures. In this paper, laboratory tests and numerical simulations are used to investigate the mechanical properties of the sandstone–concrete combined body. Uniaxial compression tests and an acoustic emission monitoring system are used to analyze the failure characteristics of the sandstone–concrete sample and to validate the accuracy of the numerical model. The mechanical properties of the composite body were further analyzed by integrating energy and damage theories. The results of the sandstone–concrete study suggest that the combined sandstone–concrete body exhibits synergistic deformation and failure when subjected to uniaxial compression. The peak stress and elastic modulus fall between those of sandstone and concrete. The interface's shape causes the stress in the y-direction to transition from tensile stress to compressive stress. Energy is stored before reaching the peak stress and released after reaching the peak stress. The damage curve indicates that the damage increases gradually with the strain, and it results in plastic failure. In the numerical simulation of triaxial compression, the stress and displacement at the interface are evenly distributed. Compared to uniaxial compression, the energy of each component is higher and shows a linear positive correlation with confining pressure. Additionally, the rate of energy dissipation increases with higher confining pressure. The damage variable also increases with the increase in confining pressure, and the plastic failure process is also apparent under triaxial compression.
Epidemiology of fungal infection in COVID 19 in Spain during 2020 and 2021: a nationwide study
Authors: López-Herrero R. , Sánchez-de Prada L. , Tamayo-Velasco A. , Heredia-Rodríguez M. , Bardají Carrillo M. , Jorge Monjas P. , de la Varga-Martínez O. , Resino S. , Sarmentero-López de Quintana G. , Gómez-Sánchez E. , Tamayo E. 
Published: March 2024

AbstractWe realize a nationwide population-based retrospective study to analyze the characteristics and risk factors of fungal co-infections in COVID-19 hospitalized patients as well as describe their causative agents in the Spanish population in 2020 and 2021. Data were obtained from records in the Minimum Basic Data Set of the National Surveillance System for Hospital Data in Spain, provided by the Ministry of Health, and annually published with two years lag. The assessment of the risk associated with the development of healthcare-associated fungal co-infections was assessed using an adjusted logistic regression model. The incidence of fungal co-infection in COVID-19 hospitalized patients was 1.41%. The main risk factors associated were surgery, sepsis, age, male gender, obesity, and COPD. Co-infection was associated with worse outcomes including higher in-hospital and in ICU mortality, and higher length of stay. Candida spp. and Aspergillus spp. were the microorganisms more frequent. This is the first study analyzing fungal coinfection at a national level in hospitalized patients with COVID-19 in Spanish population and one of the few studies available that demonstrate that surgery was an independent risk factor of Aspergillosis coinfection in COVID-19 patients.
Determinants of pesticides use among tomato farmers in the Bono and Ahafo regions of Ghana
Authors: Bandanaa Joseph , Bosomtwe Augustine , Danson-Anokye Alexander , Adjei Eric , Bissah Matilda , Kotey Daniel A. 
Published: March 2024

AbstractTomato production plays a crucial role in the livelihoods of farmers and agricultural households in the forest savanna transitional belt of Ghana. However, the success of tomato cultivation is hindered by the presence of insect pests and diseases, necessitating the use of agricultural inputs. This study aimed to identify the pesticides used in tomato farming, assess their World Health Organization (WHO) active ingredient hazard class, determine the precautionary behaviour associated with pesticide use by tomato farmers, and elucidate the socio-economic factors influencing pesticide usage in the Bono and Ahafo regions of Ghana. A multistage sampling procedure was employed to select 1009 respondents, who were administered a structured questionnaire. Descriptive statistics and logistic regression models were used to analyse the collected data. The results revealed that tomato farmers utilized 15 types of insecticides (e.g., lambda and chlorpyrifos ethyl based), 8 types of fungicides (e.g., mancozeb and sulphur + copper based), and 6 types of weedicides (mostly glyphosate based) on their crops. Notably, four insecticides and two fungicides types were found to be unregistered products. Lambda-cyhalothrin-based insecticides and mancozeb-based fungicides were predominantly used by the farmers. The assessed pesticides exhibited varying levels of hazard, ranging from slight to moderate. The study found that farmer training was a significant driver influencing insecticide use, while the educational level of farmers and average yield played important roles in determining fungicide use. Socio-economic factors such as being the head of the household, employing farm workers, the cultivated tomato variety, and farmer training influenced weedicide use. The type of tomato variety cultivated emerged as the primary socio-economic driver of pesticide use. The study recommended the establishment and implementation of a systematic monitoring regime for pesticide product marketing and use, with the aim of reducing the utilization of unregistered products by farmers. Implementing these measures supports sustainable tomato farming in the Bono and Ahafo regions of Ghana.