bluuebunny/crossref_metadata_2025_split huggingface dataset:
Recent progress on gene-deleted live-attenuated African swine fever virus vaccines
Authors: Vu Hiep L. X. , McVey D. Scott 
Published: March 2024

AbstractAfrican Swine Fever (ASF) is a highly lethal viral disease in swine, with mortality rates approaching 100%. The disease has spread to many swine-producing countries, leading to significant economic losses and adversely impacting global food security. Extensive efforts have been directed toward developing effective ASF vaccines. Among the vaccinology approaches tested to date, live-attenuated virus (LAV) vaccines produced by rational deleting virulence genes from virulent African Swine Fever Virus (ASFV) strains have demonstrated promising safety and efficacy in experimental and field conditions. Many gene-deleted LAV vaccine candidates have been generated in recent years. The virulence genes targeted for deletion from the genome of virulent ASFV strains can be categorized into four groups: Genes implicated in viral genome replication and transcription, genes from the multigene family located at both 5′ and 3′ termini, genes participating in mediating hemadsorption and putative cellular attachment factors, and novel genes with no known functions. Some promising LAV vaccine candidates are generated by deleting a single viral virulence gene, whereas others are generated by simultaneously deleting multiple genes. This article summarizes the recent progress in developing and characterizing gene-deleted LAV vaccine candidates.
Cell constriction requires processive septal peptidoglycan synthase movement independent of FtsZ treadmilling in Staphylococcus aureus
Authors: Schäper Simon , Brito António D. , Saraiva Bruno M. , Squyres Georgia R. , Holmes Matthew J. , Garner Ethan C. , Hensel Zach , Henriques Ricardo , Pinho Mariana G. 
Published: March 2024

AbstractBacterial cell division requires recruitment of peptidoglycan (PG) synthases to the division site by the tubulin homologue, FtsZ. Septal PG synthases promote septum growth. FtsZ treadmilling is proposed to drive the processive movement of septal PG synthases and septal constriction in some bacteria; however, the precise mechanisms spatio-temporally regulating PG synthase movement and activity and FtsZ treadmilling are poorly understood. Here using single-molecule imaging of division proteins in the Gram-positive pathogen Staphylococcus aureus, we showed that the septal PG synthase complex FtsW/PBP1 and its putative activator protein, DivIB, move with similar velocity around the division site. Impairing FtsZ treadmilling did not affect FtsW or DivIB velocities or septum constriction rates. Contrarily, PG synthesis inhibition decelerated or stopped directional movement of FtsW and DivIB, and septum constriction. Our findings suggest that a single population of processively moving FtsW/PBP1 associated with DivIB drives cell constriction independently of FtsZ treadmilling in S. aureus.
Spatially organized cellular communities form the developing human heart
Authors: Farah Elie N. , Hu Robert K. , Kern Colin , Zhang Qingquan , Lu Ting-Yu , Ma Qixuan , Tran Shaina , Zhang Bo , Carlin Daniel , Monell Alexander , Blair Andrew P. , Wang Zilu , Eschbach Jacqueline , Li Bin , Destici Eugin , Ren Bing , Evans Sylvia M. , Chen Shaochen , Zhu Quan , Chi Neil C. 
Published: March 2024

AbstractThe heart, which is the first organ to develop, is highly dependent on its form to function1,2. However, how diverse cardiac cell types spatially coordinate to create the complex morphological structures that are crucial for heart function remains unclear. Here we integrated single-cell RNA-sequencing with high-resolution multiplexed error-robust fluorescence in situ hybridization to resolve the identity of the cardiac cell types that develop the human heart. This approach also provided a spatial mapping of individual cells that enables illumination of their organization into cellular communities that form distinct cardiac structures. We discovered that many of these cardiac cell types further specified into subpopulations exclusive to specific communities, which support their specialization according to the cellular ecosystem and anatomical region. In particular, ventricular cardiomyocyte subpopulations displayed an unexpected complex laminar organization across the ventricular wall and formed, with other cell subpopulations, several cellular communities. Interrogating cell–cell interactions within these communities using in vivo conditional genetic mouse models and in vitro human pluripotent stem cell systems revealed multicellular signalling pathways that orchestrate the spatial organization of cardiac cell subpopulations during ventricular wall morphogenesis. These detailed findings into the cellular social interactions and specialization of cardiac cell types constructing and remodelling the human heart offer new insights into structural heart diseases and the engineering of complex multicellular tissues for human heart repair.
APOE4/4 is linked to damaging lipid droplets in Alzheimer’s disease microglia
Authors: Haney Michael S. , Pálovics Róbert , Munson Christy Nicole , Long Chris , Johansson Patrik K. , Yip Oscar , Dong Wentao , Rawat Eshaan , West Elizabeth , Schlachetzki Johannes C. M. , Tsai Andy , Guldner Ian Hunter , Lamichhane Bhawika S. , Smith Amanda , Schaum Nicholas , Calcuttawala Kruti , Shin Andrew , Wang Yung-Hua , Wang Chengzhong , Koutsodendris Nicole , Serrano Geidy E. , Beach Thomas G. , Reiman Eric M. , Glass Christopher K. , Abu-Remaileh Monther , Enejder Annika , Huang Yadong , Wyss-Coray Tony 
Published: March 2024

AbstractSeveral genetic risk factors for Alzheimer’s disease implicate genes involved in lipid metabolism and many of these lipid genes are highly expressed in glial cells1. However, the relationship between lipid metabolism in glia and Alzheimer’s disease pathology remains poorly understood. Through single-nucleus RNA sequencing of brain tissue in Alzheimer’s disease, we have identified a microglial state defined by the expression of the lipid droplet-associated enzyme ACSL1 with ACSL1-positive microglia being most abundant in patients with Alzheimer’s disease having theAPOE4/4genotype. In human induced pluripotent stem cell-derived microglia, fibrillar Aβ inducesACSL1expression, triglyceride synthesis and lipid droplet accumulation in an APOE-dependent manner. Additionally, conditioned media from lipid droplet-containing microglia lead to Tau phosphorylation and neurotoxicity in an APOE-dependent manner. Our findings suggest a link between genetic risk factors for Alzheimer’s disease with microglial lipid droplet accumulation and neurotoxic microglia-derived factors, potentially providing therapeutic strategies for Alzheimer’s disease.
Blueprinting extendable nanomaterials with standardized protein blocks
Authors: Huddy Timothy F. , Hsia Yang , Kibler Ryan D. , Xu Jinwei , Bethel Neville , Nagarajan Deepesh , Redler Rachel , Leung Philip J. Y. , Weidle Connor , Courbet Alexis , Yang Erin C. , Bera Asim K. , Coudray Nicolas , Calise S. John , Davila-Hernandez Fatima A. , Han Hannah L. , Carr Kenneth D. , Li Zhe , McHugh Ryan , Reggiano Gabriella , Kang Alex , Sankaran Banumathi , Dickinson Miles S. , Coventry Brian , Brunette T. J. , Liu Yulai , Dauparas Justas , Borst Andrew J. , Ekiert Damian , Kollman Justin M. , Bhabha Gira , Baker David 
Published: March 2024

AbstractA wooden house frame consists of many different lumber pieces, but because of the regularity of these building blocks, the structure can be designed using straightforward geometrical principles. The design of multicomponent protein assemblies, in comparison, has been much more complex, largely owing to the irregular shapes of protein structures1. Here we describe extendable linear, curved and angled protein building blocks, as well as inter-block interactions, that conform to specified geometric standards; assemblies designed using these blocks inherit their extendability and regular interaction surfaces, enabling them to be expanded or contracted by varying the number of modules, and reinforced with secondary struts. Using X-ray crystallography and electron microscopy, we validate nanomaterial designs ranging from simple polygonal and circular oligomers that can be concentrically nested, up to large polyhedral nanocages and unbounded straight ‘train track’ assemblies with reconfigurable sizes and geometries that can be readily blueprinted. Because of the complexity of protein structures and sequence–structure relationships, it has not previously been possible to build up large protein assemblies by deliberate placement of protein backbones onto a blank three-dimensional canvas; the simplicity and geometric regularity of our design platform now enables construction of protein nanomaterials according to ‘back of an envelope’ architectural blueprints.
Neural and behavioural state switching during hippocampal dentate spikes
Authors: Farrell Jordan S. , Hwaun Ernie , Dudok Barna , Soltesz Ivan 
Published: March 2024

Abstract
Distinct brain and behavioural states are associated with organized neural population dynamics that are thought to serve specific cognitive functions1–3. Memory replay events, for example, occur during synchronous population events called sharp-wave ripples in the hippocampus while mice are in an ‘offline’ behavioural state, enabling cognitive mechanisms such as memory consolidation and planning4–11. But how does the brain re-engage with the external world during this behavioural state and permit access to current sensory information or promote new memory formation? Here we found that the hippocampal dentate spike, an understudied population event that frequently occurs between sharp-wave ripples12, may underlie such a mechanism. We show that dentate spikes are associated with distinctly elevated brain-wide firing rates, primarily observed in higher order networks, and couple to brief periods of arousal. Hippocampal place coding during dentate spikes aligns to the mouse’s current spatial location, unlike the memory replay accompanying sharp-wave ripples. Furthermore, inhibiting neural activity during dentate spikes disrupts associative memory formation. Thus, dentate spikes represent a distinct brain state and support memory during non-locomotor behaviour, extending the repertoire of cognitive processes beyond the classical offline functions.
Numerical analyses for three-dimensional face stability of circular tunnels in purely cohesive soils with linearly increasing strength
Authors: Huang Bing , Yu Daidai , Zhao Yinting , Zhu Junfeng 
Published: March 2024

AbstractThe tunnel face stability in purely cohesive soils with linearly increasing strength was investigated using three-dimensional finite element limit analysis (FELA). Both the collapse (active failure) and blow-out (passive failure) of the tunnel face were considered in the analysis. The rigorous upper bound (UB) and lower bound (LB) solutions of the load factor were calculated with a wide range of ground conditions to cover a broad scope of practical application. The results showed that the whole surface of the face is at failure in the collapse case; while in the blow-out case, there exists a gradual evolution process from partial failure to global failure within the tunnel face with increasing buried depth. Later, based on 960 finite element limit analysis results, a series of practical equations were proposed for tunnel face stability analysis in purely cohesive soils. These equations can be employed to quickly calculate the UB and LB solutions of the limit support pressure and the stability number of a tunnel face in both the collapse and blow-out cases. Finally, the calculation results from these equations were compared with those from previous studies in detail. The comparisons showed that the proposed equations make an improvement over existing methods and can be used as an efficient tool in practical engineering.
Geohazard assessment of Mexico City’s Metro system derived from SAR interferometry observations
Authors: Solano-Rojas Darío , Wdowinski Shimon , Cabral-Cano Enrique , Osmanoğlu Batuhan 
Published: March 2024

AbstractLand subsidence rates in Mexico City reach 500 mm/year, causing progressive damage to the city’s core infrastructure, including the Metro system. A deadly overpass collapse in 2021, along a Metro line that had operated for less than 10 years, brought subsidence-related structural damage to the attention of the system’s authorities and led to major repairs to two of the twelve Metro lines. Still, the need for quantifying the magnitude and extent of subsidence affecting the Metro system’s widespread infrastructure prevails. Using a wealth of satellite radar interferometry observations, levelling surveys, subsurface profiles, linear gradient and differential displacement analyses, and structural-engineering parameters, we assess the vulnerability of the Metro system’s street-level and elevated segments to land subsidence. Our results reveal that high subsidence velocity gradients occur over sharp transitional zones between stable and fast-subsiding areas, reaching values of 1 $$\times \,10 ^{-3}$$

×

10

-
3

year$$^{-1}$$

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1

, resulting in slope changes up to 3.5% over a 20-year period and differential displacements between columns. Our findings suggest locations where the consequences of subsidence have compromised the train’s braking safety design, increased railway flooding hazard, produced railway bending, and reduced the conceived 50-year service life of the Metro’s elevated overpasses.
Optimization of Chinese land spatial pattern in the transformation process of resource-based cities: a case study in Tongling City, China
Authors: Ye Yun , Qin Yan , Yu Ran , Wu Qun 
Published: March 2024

AbstractOptimizing the spatial layout of the national territory is crucial for realizing the transformation and development of resource-oriented cities in the context of high-quality development in the new period. This paper takes Tongling City as a case study, based on the analysis of the historical development foundation, then uses the SD-FLUS comprehensive model to carry out a systematic analysis of the transformation in five dimensions of economy, society, population, science and technology, resources and environment, and discusses the optimization of spatial pattern under the contextual simulation. The conclusions are as follows: ① The hierarchical framework of “system-indicator-element” is not only internally interconnected, but also inextricably linked with the relationship between the various categories of the land use system. ② Decrease of cropland, forest, water, grassland, and barren decreases from the economic development, social progress, and comprehensive development, and there is a small increase in the area under the scenario of resource and environmental protection, and the direction of the change of the impervious is in the opposite direction. ③ Cultivated land is retained in situ and concentrated to a small extent, forested land is reduced to a small extent while the status quo is maintained, and the Yangtze River water system will be retained and protected to a large extent, but part of the waters of Zongyang County will give way to the expansion of construction land under the development objectives of the new county. Building land will be expanded and extended to the northeast in the original site area, while the southwest corner of the original county center will be expanded to some extent in Zongyang County to promote the county’s economic development.
Isolation and characterization of a newly discovered plant growth-promoting endophytic fungal strain from the genus Talaromyces
Authors: Kharkwal Amit C. , Joshi Hemesh , Shandilya Cheshta , Dabral Surbhi , Kumar Niraj , Varma Ajit 
Published: March 2024

AbstractIn the Kandi zone of Punjab, India, root and rhizospheric soil samples were collected from the local vegetation near the Shivalik mountain foothills. Fifteen fungal colonies exhibiting distinct cultural morphology on Potato Dextrose Agar (PDA) plates were selected for plant–microbe interaction studies. Among these, the isolate HNB9 was identified as a nonpathogenic root colonizer. Morphological and molecular analyses confirmed HNB9 as Talaromyces albobiverticillius, characterized by the secretion of a red pigment as a secondary metabolite. Plants colonized with T. albobiverticillius HNB9 exhibited enhanced growth, manifesting in increased shoot and root length compared to untreated controls. This study unveiled the first evidence that a species from the Talaromyces genus, specifically T. albobiverticillius, possesses dual capabilities of root colonization and plant growth promotion. Moreover, HNB9 demonstrated the production of plant growth-regulating compounds like Indole Acetic Acid (IAA) and proficient solubilization of crucial nutrients (Phosphorous, Zinc, and Silica) through plate culture methods. This finding represents a significant contribution to the understanding of root-colonizing fungi with plant growth-promoting attributes, challenging the existing knowledge gap within the Talaromyces genus.
7 Dimensions of software change patterns
Authors: Janke Mario , Mäder Patrick 
Published: March 2024

AbstractEvolving software is a highly complex and creative problem in which a number of different strategies are used to solve the tasks at hand. These strategies and reoccurring coding patterns can offer insights into the process. However, they can be highly project or even task-specific. We aim to identify code change patterns in order to draw conclusions about the software development process. For this, we propose a novel way to calculate high-level file overarching diffs, and a novel way to parallelize pattern mining. In a study of 1000 Java projects, we mined and analyzed a total of 45,000 patterns. We present 13 patterns, showing extreme points of the 7 pattern categories we identified. We found that a large number of high-level change patterns exist and occur frequently. The majority of mined patterns were associated with a specific project and contributor, where and by whom it was more likely to be used. While a large number of different code change patterns are used, only a few, mostly unsurprising ones, are common under all circumstances. The majority of code change patterns are highly specific to different context factors that we further explore.
Titanate-based high-entropy perovskite oxides relaxor ferroelectrics
Authors: Bunpang Ketkaeo , Singkammo Suparat , Cann David P. , Raengthon Natthaphon 
Published: March 2024

AbstractDifferent combinations of monovalent and trivalent A-cations in high-entropy perovskite oxides (HEPOs) were investigated. The multicomponent (A′0.2A″0.2Ba0.2Sr0.2Ca0.2)TiO3 (A′ = Na+, K+, A″ = Bi3+, La3+) perovskite compounds were successfully synthesized by solid-state reaction method persisting average cubic perovskite phase. The trivalent cation exhibited distinct effects on local structure, dielectric properties and relaxor ferroelectric behavior. Highly dense ceramics (> 95%), high dielectric constant (~ 3000), low dielectric loss (~ 0.1), and relaxor ferroelectric characteristics were obtained in the compound containing Bi3+. The La3+ containing compounds revealed lower dielectric constant, higher dielectric loss and linear dielectric behavior. The effect of monovalent cation on the dielectric properties was minimal. However, it affected relaxor ferroelectric behavior at elevated temperatures and conduction behavior at high temperatures. The (K0.2Bi0.2Ba0.2Sr0.2Ca0.2)TiO3 ceramic maintained the relaxor ferroelectric behavior with low PREM at high temperatures suggesting more stable relaxor ferroelectric characteristics than that of the (Na0.2Bi0.2Ba0.2Sr0.2Ca0.2)TiO3. Moreover, between these two compounds, the homogeneous electrical characteristics could be obtained from the compound consisting of K + and Bi + at A-site. This study suggests that tuning the chemical composition, particularly choosing appropriate combination of mono/trivalent cations in high entropy perovskite oxides, could be the effective approach to develop high-performance relaxor ferroelectrics with the desired properties.
KSRP improves pancreatic beta cell function and survival
Authors: Barssotti Leticia , Soares Gabriela Moreira , Marconato-Júnior Emílio , Lourençoni Alves Bruna , Oliveira Kênia Moreno , Carneiro Everardo Magalhães , Boschero Antonio Carlos , Barbosa Helena Cristina Lima 
Published: March 2024

AbstractImpaired insulin production and/or secretion by pancreatic beta cells can lead to high blood glucose levels and type 2 diabetes (T2D). Therefore, investigating new proteins involved in beta cell response to stress conditions could be useful in finding new targets for therapeutic approaches. KH-type splicing regulatory protein (KSRP) is a protein usually involved in gene expression due to its role in post-transcriptional regulation. Although there are studies describing the important role of KSRP in tissues closely related to glucose homeostasis, its effect on pancreatic beta cells has not been explored so far. Pancreatic islets from diet-induced obese mice (C57BL/6JUnib) were used to determine KSRP expression and we also performed in vitro experiments exposing INS-1E cells (pancreatic beta cell line) to different stressors (palmitate or cyclopiazonic acid—CPA) to induce cellular dysfunction. Here we show that KSRP expression is reduced in all the beta cell dysfunction models tested. In addition, when manipulated to knock down KSRP, beta cells exhibited increased death and impaired insulin secretion, whereas KSRP overexpression prevented cell death and increased insulin secretion. Taken together, our findings suggest that KSRP could be an important target to protect beta cells from impaired functioning and death.
Maternal attachment security modulates the relationship between vulnerability to anxiety and attentional bias to threat in healthy children
Authors: Raymond Catherine , Cernik Rebecca , Beaudin Myriam , Arcand Maryse , Pichette Florence , Marin Marie-France 
Published: March 2024

AbstractThis study aimed to investigate whether attentional bias to threat, commonly observed in clinically anxious children, also manifests in healthy children, potentially aiding the early detection of at-risk individuals. Additionally, it sought to explore the moderating role of parent–child attachment security on the association between vulnerability factors (anxiety sensitivity, intolerance of uncertainty, perseverative cognitions) as indicators of vulnerability to anxiety, and attentional bias towards threat in healthy children. A total of 95 children aged 8 to 12 years completed the Visual Search Task to assess attentional bias. Vulnerability to anxiety was measured using a composite score derived from the Childhood Anxiety Sensitivity Index, Intolerance of Uncertainty Scale for Children, and Perseverative Thinking Questionnaire. Parent–child attachment security was assessed using the Security Scale-Child Self-Report. Analyses revealed that higher vulnerability to anxiety was associated with faster detection of anger-related stimuli compared to neutral ones, and this association was further influenced by high maternal security. These findings in healthy children suggest an interaction between specific factors related to anxiety vulnerability and the security of the mother–child relationship, leading to cognitive patterns resembling those seen in clinically anxious individuals. These results hold promise for early identification of children at risk of developing anxiety disorders.